[gmx-users] LJ - SR and Coulbom - SR mdp options
Dear Gmx Users, I want to obtain average Protein-Ligand SR electrostatics and LJ energy values using g_energy from NPT equlibration with position restraints. I used energygrps = Protein LIG However, when I run g_energy -f npt.edr -s npt.tpr I see neither Protein-LIG for any of them. Would you please advise? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
How about applying position restarints with a strong force constant? What is less computationally expensive: position restrained, freezing the whole molecule? The nanotube should be rigid... Shall I place the edged of the tube on the box edge as well and use pbc=xyz and periodic molecules = yes? Thanks, Steven On Thu, Sep 26, 2013 at 9:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/26/13 12:05 PM, Dr. Vitaly Chaban wrote: Steven - I would use a simple harmonic bond. Note that either in the case of the distance restraint or harmonic interaction approach, both the CNT and the molecule to which it is tethered need to be in the same [moleculetype], so run pdb2gmx (or whatever you are using) with care. -Justin Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann s.neuman...@gmail.com wrote: Thank you for this. And also I wish to attach a chain to my nanotube so they will be both able to move together. Is that a matter of distance restraints between nanotube atom and first atom of my chain or again - LINCS? Both chain and nanotube are made of the same type of 8 type of atoms. Please, advise. Steven On Thu, Sep 26, 2013 at 3:19 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: I am just curious why the system would explode without periodic_molecules = yes. If the PBC procedure is applied before harmonic bond potential is calculated, than the opposite nanotube atoms should be (already) seen as neighboring. This looks the same as the solvent molecule, one atom of which crossed the box boundary. No? Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/26/13 8:39 AM, Steven Neumann wrote: Dear Gmx Users, I have my carbon nanotube and I wish to make it infinite in lenght. Which mdp options whall be used? pbc = xy and z is the infinite dimension? another issue: Would you apply bonds between carbon atoms within the nanotube or constraints using LINCS? Which of them is less computationally expensive for the run? Use pbc = xyz in conjunction with periodic_molecules = yes otherwise the topology gets messed up trying to form unreasonable bonds. The periodic_molecules keyword in the .mdp allows for bonds to be maintained over PBC. I remember a very old post somewhere in the archive that said one should not apply pressure coupling along the axis of the nanotube, due to some difficulties with maintaining the bonded geometry, but since I have never done CNT simulations, take the fact that I'm just repeating what I've heard for what it's worth :) Constraints always come with the cost of communication, so I would imagine harmonic bonds are less expensive. I really don't see constraints as a limiting factor for performance, though. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edujalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support
Re: [gmx-users] carbon nanotube - ifnite in length ?
Thanks a lot. You the bond as a distance between atoms? I wish to avoid bonds as they are not necessary...just position restraint. What would be the force constant? I tried 1000 once without bonds and my atoms were moving a bit... Steven On Thu, Oct 10, 2013 at 2:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/10/13 9:21 AM, Steven Neumann wrote: How about applying position restarints with a strong force constant? What is less computationally expensive: position restrained, freezing the whole molecule? The nanotube should be rigid... Shall I place the edged of the You shouldn't see any real performance gain or loss by applying either restraints or freezing. tube on the box edge as well and use pbc=xyz and periodic molecules = yes? The box size needs to be (length of tube) + (bond length). If you place the carbon atoms at the box edge, they overlap and the system blows up. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] - is there any gmx tool to exclude interactions within the given molecule so 1 with all 1200, 2 with all 1200...etc... 1200 with all 1200? Steven On Thu, Oct 10, 2013 at 2:34 PM, Steven Neumann s.neuman...@gmail.comwrote: Thanks a lot. You the bond as a distance between atoms? I wish to avoid bonds as they are not necessary...just position restraint. What would be the force constant? I tried 1000 once without bonds and my atoms were moving a bit... Steven On Thu, Oct 10, 2013 at 2:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/10/13 9:21 AM, Steven Neumann wrote: How about applying position restarints with a strong force constant? What is less computationally expensive: position restrained, freezing the whole molecule? The nanotube should be rigid... Shall I place the edged of the You shouldn't see any real performance gain or loss by applying either restraints or freezing. tube on the box edge as well and use pbc=xyz and periodic molecules = yes? The box size needs to be (length of tube) + (bond length). If you place the carbon atoms at the box edge, they overlap and the system blows up. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
Thanks. I will place them then within the distance from the box edge = distance between atoms within the tube right? I can create bonds and use harmonic spring constant like for backbone protein atoms...but whats the point when they do not move anyway? I am using NVT. Steven On Thu, Oct 10, 2013 at 2:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/10/13 9:34 AM, Steven Neumann wrote: Thanks a lot. You the bond as a distance between atoms? I wish to avoid bonds as they are not necessary...just position restraint. What would be the force constant? I tried 1000 once without bonds and my atoms were moving a bit... If you don't have bonds, then there is no point using periodic_molecules. Still, the point stands that you cannot place atoms at the box edge, because they will overlap via PBC regardless of periodic_molecules. Using freezegrps causes artifacts, especially with pressure coupling, so if you want to model the tubes as rigid, then the only real option that I can think of is to simply increase the force constant for the restraints. I don't particularly understand this approach, as people have done tons of simulations of nanotubes with normal bonded geometry. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
Thank you. Would both be equal in terms of gaining computational time? Steven On Thu, Oct 10, 2013 at 2:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/10/13 9:39 AM, Steven Neumann wrote: And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] - is there any gmx tool to exclude interactions within the given molecule so 1 with all 1200, 2 with all 1200...etc... 1200 with all 1200? No, but it's a simple script to write since you just iterate through a counter. Alternatively, just use a [nonbond_params] directive to set the interactions of the atoms to zero (unless they have charges, in which case you do need [exclusions]). -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
Thank you. I do not have any explicit solvent in my system. I included the solvent in nonbonded parameters so not even implicit. Steven On Thu, Oct 10, 2013 at 2:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/10/13 9:44 AM, Steven Neumann wrote: Thanks. I will place them then within the distance from the box edge = distance between atoms within the tube right? I can create bonds and use harmonic spring constant like for backbone protein atoms...but whats the point when they do not move anyway? I am using NVT. If your goal is simply to have some series of atoms in a cylindrical overall shape that do not move, there is no purpose to using bonds. NVT will still suffer from problems with frozen groups; the temperature will not be right because after a collision with a solvent atom, the tube atom by definition cannot move. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
Thanks a lot. I will use position restraints then with a strong force constant, no bonds and place the edge atoms within half of distance between them from the box edge. Is that correct? Steven On Thu, Oct 10, 2013 at 2:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/10/13 9:54 AM, Steven Neumann wrote: Thank you. I do not have any explicit solvent in my system. I included the solvent in nonbonded parameters so not even implicit. Well, presumably you have other things in the system, otherwise you're simulating an inert tube of non-interacting atoms, which I doubt is useful for anything. Basically what I'm trying to say is freezegrps is listed as a non-equilibrium option for a reason - it does not correspond to physical reality and can seriously perturb your system in bad ways. It's really only useful for equilibrating problematic systems, and nothing else IMHO. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
Thank you! Steven On Thu, Oct 10, 2013 at 3:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/10/13 10:01 AM, Steven Neumann wrote: Thanks a lot. I will use position restraints then with a strong force constant, no bonds and place the edge atoms within half of distance between them from the box edge. Is that correct? Seems reasonable. One way to find out... -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Steered MD
Dear Gromacs Users, I am trying to look for some references regarding the SMD. I found one which tells about logarithmically dependency between the Rupture force (maximum pulling force) obtained from SMD and the pulling rate. Just wondering whether you are aware (or tested) the dependency between rupture force and harmonic spring constant? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] carbon nanotube - ifnite in length ?
Dear Gmx Users, I have my carbon nanotube and I wish to make it infinite in lenght. Which mdp options whall be used? pbc = xy and z is the infinite dimension? another issue: Would you apply bonds between carbon atoms within the nanotube or constraints using LINCS? Which of them is less computationally expensive for the run? Thank you in advance, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
Thank you for this. And also I wish to attach a chain to my nanotube so they will be both able to move together. Is that a matter of distance restraints between nanotube atom and first atom of my chain or again - LINCS? Both chain and nanotube are made of the same type of 8 type of atoms. Please, advise. Steven On Thu, Sep 26, 2013 at 3:19 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: I am just curious why the system would explode without periodic_molecules = yes. If the PBC procedure is applied before harmonic bond potential is calculated, than the opposite nanotube atoms should be (already) seen as neighboring. This looks the same as the solvent molecule, one atom of which crossed the box boundary. No? Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/26/13 8:39 AM, Steven Neumann wrote: Dear Gmx Users, I have my carbon nanotube and I wish to make it infinite in lenght. Which mdp options whall be used? pbc = xy and z is the infinite dimension? another issue: Would you apply bonds between carbon atoms within the nanotube or constraints using LINCS? Which of them is less computationally expensive for the run? Use pbc = xyz in conjunction with periodic_molecules = yes otherwise the topology gets messed up trying to form unreasonable bonds. The periodic_molecules keyword in the .mdp allows for bonds to be maintained over PBC. I remember a very old post somewhere in the archive that said one should not apply pressure coupling along the axis of the nanotube, due to some difficulties with maintaining the bonded geometry, but since I have never done CNT simulations, take the fact that I'm just repeating what I've heard for what it's worth :) Constraints always come with the cost of communication, so I would imagine harmonic bonds are less expensive. I really don't see constraints as a limiting factor for performance, though. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] The optimal PME mesh load for parallel simulations is below 0.5
DEa Users, My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want to use PME in my mdp: rcoulomb = 2.0 coulombtype = PME pme_order= 4 fourierspacing = 0.12 The cutoff needs to stay like this, I have my own tables with VDW, bonds, angles and dihedrals. i got the NOTE: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing what setting would you suggest to use on 8 CPUs? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The optimal PME mesh load for parallel simulations is below 0.5
Thank you! Would you suggest just a cut-off for coulmb? Steven On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:03 AM, Steven Neumann wrote: DEa Users, My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want to use PME in my mdp: rcoulomb = 2.0 coulombtype = PME pme_order= 4 fourierspacing = 0.12 The cutoff needs to stay like this, I have my own tables with VDW, bonds, angles and dihedrals. i got the NOTE: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing what setting would you suggest to use on 8 CPUs? I would suggest not using PME :) The problem is PME is extremely inefficient in vacuo because it spends a lot of time doing nothing due to the empty space. Moreover, you're not likely really simulating in vacuo at that point because you've got PBC and therefore are really doing a simulation in more of a diffuse crystal environment, so there are probably artifacts. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The optimal PME mesh load for parallel simulations is below 0.5
Thank you. i am using my own vdw tables so need a cut off. On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:11 AM, Steven Neumann wrote: Thank you! Would you suggest just a cut-off for coulmb? Not a finite one. The best in vacuo settings are: pbc = no rlist = 0 rvdw = 0 rcoulomb = 0 nstlist = 0 vdwtype = cutoff coulombtype = cutoff -Justin On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:03 AM, Steven Neumann wrote: DEa Users, My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want to use PME in my mdp: rcoulomb = 2.0 coulombtype = PME pme_order= 4 fourierspacing = 0.12 The cutoff needs to stay like this, I have my own tables with VDW, bonds, angles and dihedrals. i got the NOTE: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing what setting would you suggest to use on 8 CPUs? I would suggest not using PME :) The problem is PME is extremely inefficient in vacuo because it spends a lot of time doing nothing due to the empty space. Moreover, you're not likely really simulating in vacuo at that point because you've got PBC and therefore are really doing a simulation in more of a diffuse crystal environment, so there are probably artifacts. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The optimal PME mesh load for parallel simulations is below 0.5
Sorry it is a vacuum but I included implicit solvent in vdw parameters...So I need pbc as well. On Wed, Sep 4, 2013 at 3:18 PM, Steven Neumann s.neuman...@gmail.comwrote: Thank you. i am using my own vdw tables so need a cut off. On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:11 AM, Steven Neumann wrote: Thank you! Would you suggest just a cut-off for coulmb? Not a finite one. The best in vacuo settings are: pbc = no rlist = 0 rvdw = 0 rcoulomb = 0 nstlist = 0 vdwtype = cutoff coulombtype = cutoff -Justin On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:03 AM, Steven Neumann wrote: DEa Users, My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want to use PME in my mdp: rcoulomb = 2.0 coulombtype = PME pme_order= 4 fourierspacing = 0.12 The cutoff needs to stay like this, I have my own tables with VDW, bonds, angles and dihedrals. i got the NOTE: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing what setting would you suggest to use on 8 CPUs? I would suggest not using PME :) The problem is PME is extremely inefficient in vacuo because it spends a lot of time doing nothing due to the empty space. Moreover, you're not likely really simulating in vacuo at that point because you've got PBC and therefore are really doing a simulation in more of a diffuse crystal environment, so there are probably artifacts. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The optimal PME mesh load for parallel simulations is below 0.5
Thanks a lot! On Wed, Sep 4, 2013 at 3:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:44 AM, Steven Neumann wrote: Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be taken into account at infinite cutoff or omitted? As I said, setting the cutoffs to zero does not omit interactions. The zero is used to trigger infinite cutoffs. -Justin On Wed, Sep 4, 2013 at 3:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:35 AM, Steven Neumann wrote: I am not using any solvent. I mimic the presence of water by vdw tabulated potentials. I wish to see what electrostatics will change. And the coulomb cutoff = 0 will completely remove the electrostatic, right? No, it does the opposite. Setting all cutoffs to zero triggers the all-vs-all kernels, which calculate every possible interaction. -Justin On Wed, Sep 4, 2013 at 3:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:20 AM, Steven Neumann wrote: Sorry it is a vacuum but I included implicit solvent in vdw parameters...So I need pbc as well. Sorry, this doesn't make much sense to me. If you're using implicit solvent (GB), then it's by definition not vacuum. I also find the same to be true - finite cutoffs lead to artifacts in vacuo or when using GB. The only stable simulations I have produced using GB us the all-vs-all settings I showed below. Obviously, if your parameterization and tabulated interactions have different requirements, then what I said goes out the window, but using GB with PBC also suffers from artifacts. -Justin On Wed, Sep 4, 2013 at 3:18 PM, Steven Neumann s.neuman...@gmail.com wrote: Thank you. i am using my own vdw tables so need a cut off. On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:11 AM, Steven Neumann wrote: Thank you! Would you suggest just a cut-off for coulmb? Not a finite one. The best in vacuo settings are: pbc = no rlist = 0 rvdw = 0 rcoulomb = 0 nstlist = 0 vdwtype = cutoff coulombtype = cutoff -Justin On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:03 AM, Steven Neumann wrote: DEa Users, My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want to use PME in my mdp: rcoulomb = 2.0 coulombtype = PME pme_order= 4 fourierspacing = 0.12 The cutoff needs to stay like this, I have my own tables with VDW, bonds, angles and dihedrals. i got the NOTE: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing what setting would you suggest to use on 8 CPUs? I would suggest not using PME :) The problem is PME is extremely inefficient in vacuo because it spends a lot of time doing nothing due to the empty space. Moreover, you're not likely really simulating in vacuo at that point because you've got PBC and therefore are really doing a simulation in more of a diffuse crystal environment, so there are probably artifacts. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalemkul@outerbanks. ** umaryland.edu jalemkul@outerbanks.umaryla**nd.eduhttp://** umaryland.edu http://umaryland.edu jalemkul@outerbanks.**umaryla**nd.edu http://umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users **http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users ht**tp://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users **http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users **http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users h**ttp://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman
Re: [gmx-users] The optimal PME mesh load for parallel simulations is below 0.5
Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be taken into account at infinite cutoff or omitted? On Wed, Sep 4, 2013 at 3:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:35 AM, Steven Neumann wrote: I am not using any solvent. I mimic the presence of water by vdw tabulated potentials. I wish to see what electrostatics will change. And the coulomb cutoff = 0 will completely remove the electrostatic, right? No, it does the opposite. Setting all cutoffs to zero triggers the all-vs-all kernels, which calculate every possible interaction. -Justin On Wed, Sep 4, 2013 at 3:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:20 AM, Steven Neumann wrote: Sorry it is a vacuum but I included implicit solvent in vdw parameters...So I need pbc as well. Sorry, this doesn't make much sense to me. If you're using implicit solvent (GB), then it's by definition not vacuum. I also find the same to be true - finite cutoffs lead to artifacts in vacuo or when using GB. The only stable simulations I have produced using GB us the all-vs-all settings I showed below. Obviously, if your parameterization and tabulated interactions have different requirements, then what I said goes out the window, but using GB with PBC also suffers from artifacts. -Justin On Wed, Sep 4, 2013 at 3:18 PM, Steven Neumann s.neuman...@gmail.com wrote: Thank you. i am using my own vdw tables so need a cut off. On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:11 AM, Steven Neumann wrote: Thank you! Would you suggest just a cut-off for coulmb? Not a finite one. The best in vacuo settings are: pbc = no rlist = 0 rvdw = 0 rcoulomb = 0 nstlist = 0 vdwtype = cutoff coulombtype = cutoff -Justin On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:03 AM, Steven Neumann wrote: DEa Users, My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want to use PME in my mdp: rcoulomb = 2.0 coulombtype = PME pme_order= 4 fourierspacing = 0.12 The cutoff needs to stay like this, I have my own tables with VDW, bonds, angles and dihedrals. i got the NOTE: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing what setting would you suggest to use on 8 CPUs? I would suggest not using PME :) The problem is PME is extremely inefficient in vacuo because it spends a lot of time doing nothing due to the empty space. Moreover, you're not likely really simulating in vacuo at that point because you've got PBC and therefore are really doing a simulation in more of a diffuse crystal environment, so there are probably artifacts. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryla**nd.eduhttp://umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users ht**tp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users h**ttp://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/**mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/ Support/** http://www.gromacs.org/**Support/** http://www.gromacs.**org/Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search
Re: [gmx-users] The optimal PME mesh load for parallel simulations is below 0.5
I am not using any solvent. I mimic the presence of water by vdw tabulated potentials. I wish to see what electrostatics will change. And the coulomb cutoff = 0 will completely remove the electrostatic, right? On Wed, Sep 4, 2013 at 3:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:20 AM, Steven Neumann wrote: Sorry it is a vacuum but I included implicit solvent in vdw parameters...So I need pbc as well. Sorry, this doesn't make much sense to me. If you're using implicit solvent (GB), then it's by definition not vacuum. I also find the same to be true - finite cutoffs lead to artifacts in vacuo or when using GB. The only stable simulations I have produced using GB us the all-vs-all settings I showed below. Obviously, if your parameterization and tabulated interactions have different requirements, then what I said goes out the window, but using GB with PBC also suffers from artifacts. -Justin On Wed, Sep 4, 2013 at 3:18 PM, Steven Neumann s.neuman...@gmail.com wrote: Thank you. i am using my own vdw tables so need a cut off. On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:11 AM, Steven Neumann wrote: Thank you! Would you suggest just a cut-off for coulmb? Not a finite one. The best in vacuo settings are: pbc = no rlist = 0 rvdw = 0 rcoulomb = 0 nstlist = 0 vdwtype = cutoff coulombtype = cutoff -Justin On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/4/13 10:03 AM, Steven Neumann wrote: DEa Users, My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want to use PME in my mdp: rcoulomb = 2.0 coulombtype = PME pme_order= 4 fourierspacing = 0.12 The cutoff needs to stay like this, I have my own tables with VDW, bonds, angles and dihedrals. i got the NOTE: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing what setting would you suggest to use on 8 CPUs? I would suggest not using PME :) The problem is PME is extremely inefficient in vacuo because it spends a lot of time doing nothing due to the empty space. Moreover, you're not likely really simulating in vacuo at that point because you've got PBC and therefore are really doing a simulation in more of a diffuse crystal environment, so there are probably artifacts. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/Support/**Mailing_Lists http:/**/www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp
[gmx-users] Position Restrained of ions
Dear Gmx Users, i wish I could restrain some ions in my system (NA). I tried to include it in ions.itp: [ moleculetype ] ; molnamenrexcl NA1 #ifdef POSRES_NA [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 #endif But it does not work. Would you advise please? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella Sampling
Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling
They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling
But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann s.neuman...@gmail.comwrote: They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling
Thank you a lot! On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/31/13 6:52 AM, Steven Neumann wrote: But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? I can offer you nothing more than a hand-waving explanation of what I think might happen here, so take that for what it's worth. Since you explicitly asked for my thoughts, such as they are... The dissociation of the ions may be nothing more than an artifact of the pulling conditions. Have you tried different force constants and pull rates to see if this behavior is affected? On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann s.neuman...@gmail.com wrote: They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. Even though you're not explicitly pulling the ions, they are being forced to move due to the biasing potential that you are applying. I would think that sufficient sampling in each window (i.e. enough time that you might see dissociation of the ions) would provide you with enough information, but that's hard to predict. My assumption would be that the ions will absolutely impact the free energy of binding, but from what you said above, maybe that's right. Maybe it's not. Only way to find out would be to either exclude the ions or otherwise restrain their initial positions so that you get a clean reaction coordinate involving only the ligand. Then you can decompose the different contributions to the free energy of binding. -Justin On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx
Re: [gmx-users] Umbrella Sampling
I am do not want to choose different pulling conditions as I build a model for specific force constant and pulling rate in given force filed. I think restraining would help much more to then exclude the ions impact. Steven On Wed, Jul 31, 2013 at 12:49 PM, Steven Neumann s.neuman...@gmail.comwrote: Thank you a lot! On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/31/13 6:52 AM, Steven Neumann wrote: But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? I can offer you nothing more than a hand-waving explanation of what I think might happen here, so take that for what it's worth. Since you explicitly asked for my thoughts, such as they are... The dissociation of the ions may be nothing more than an artifact of the pulling conditions. Have you tried different force constants and pull rates to see if this behavior is affected? On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann s.neuman...@gmail.com wrote: They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. Even though you're not explicitly pulling the ions, they are being forced to move due to the biasing potential that you are applying. I would think that sufficient sampling in each window (i.e. enough time that you might see dissociation of the ions) would provide you with enough information, but that's hard to predict. My assumption would be that the ions will absolutely impact the free energy of binding, but from what you said above, maybe that's right. Maybe it's not. Only way to find out would be to either exclude the ions or otherwise restrain their initial positions so that you get a clean reaction coordinate involving only the ligand. Then you can decompose the different contributions to the free energy of binding. -Justin On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support
[gmx-users] Verlet cut off scheme with tabulated potentials
Dear Gmx Users, I want to run my simulations with tabulated non bonded and bonded parameters on Gromacs 4.6.3. When I ask for 16 cpus it says: that I am not able to use 16 or 8 with cut off scheme Group. So I set up cutoff-scheme = Verlet verlet-buffer-drift = 0.005 ERROR 1 [file grompp.mdp]: With Verlet lists only cut-off LJ interactions are supported ERROR 2 [file grompp.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported What are settings to use more than 1 cpu with vdw_type = user and coulomtype = User ? Please help, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Mass in GMX topology
Dear Users, Can you please write me where gromacs does read the mass of each atom: Is that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to assign different mass for two different beads of the same type in my topology. Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Mass in GMX topology
Thank you. Another question: Does RDF depends on the mass of the atom? On the one hand it gives different value of the force in equation of motion but on the other hand velocities are rescaled with a thermostat. Steven On Thu, Jul 11, 2013 at 12:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/11/13 7:54 AM, Steven Neumann wrote: Dear Users, Can you please write me where gromacs does read the mass of each atom: Is that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to assign different mass for two different beads of the same type in my topology. It is taken from [atoms]. The entries for mass in [atomtypes] are only used if the mass field is blank in the [atoms] directive, IIRC. Easy to check, of course, with gmxdump :) -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Mass in GMX topology
I have the same feeling, thank you. But in general mass can influence the equilibrium property so I guess yes. Steven On Thu, Jul 11, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/11/13 8:17 AM, Steven Neumann wrote: Thank you. Another question: Does RDF depends on the mass of the atom? On the one hand it gives different value of the force in equation of motion but on the other hand velocities are rescaled with a thermostat. My impression would be that the masses always affect the dynamics, but in this specific instance, I can't say how the outcome will change. I think it would also depend on the magnitude of change in the mass and whether or not you can sample enough to ever see a difference because of it. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Angle Distribution
Dear All, Do you know how can I calculate angular distribution of all angles in my system? Shall I specify in one index group all e.g. 80 atoms so g_angle will calculate all possibile distributions and plot it as a sum? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Angle Distribution
The other issue... I am using tables as an input in my protein coarse grained model based on atomistic simulations. I used Boltzmann inversion and fitted the curve into the 6th order polynomial then in angle_a*.xvg I used -f ' (x) so the derivative of my polynomial. My question: Do I need to use it as a function which will describe the angular potential? Can I just refine and smooth it? But how I am going to calculate the derivative? Steven On Mon, Jul 1, 2013 at 8:19 AM, Steven Neumann s.neuman...@gmail.comwrote: Dear All, Do you know how can I calculate angular distribution of all angles in my system? Shall I specify in one index group all e.g. 80 atoms so g_angle will calculate all possibile distributions and plot it as a sum? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Tabulated angles - how to use?
Dear Gmx Users, It is described how to use tabulated bonds/angles/dihedrals in 4.2.13 manual. I wish to use tables with angles table_a1.xvg, table_a2.xvg However it is not described which function to use in [ angles ]. It is said about [ bonds ] function 8 or 9 but no angles... Can anyone tell me please? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Can't read 1048576 bytes of 'pullx500.xvg' to compute checksum.
Dear Users, I know this error has been discussed many times but the outcome from mdrun -pf and -px stopped at the same time which is 39470 ps. Somehow gromacs caanot read pullx500.xvg but no clue why. I tried dos2gmx and still the same error occur. As I do not care about pullx500.xvg I run grompp again to change the tpr file and set pull_nstxout = 0 then run from the checkpoint but then the error occurs that 4 out of 5 files to append are only present. Can you advise please? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Can't read 1048576 bytes of 'pullx500.xvg' to compute checksum.
Thank you for this. I run this simulation from scratch, will try it next time thought. Steven On Tue, Jun 25, 2013 at 11:26 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: I had this some time ago and cant remember everything, other than its a format problem. My end solution that worked was to simply cut and past in columns the entire pullf into one .xvg, say in gnumeric retaining an origional header, than read it into xmgrace, and then just write it out from xmgrace again to file xxx.xvg then it worked. I still could not find out why, and spent hours making sure everthing had same space numbers, or tab spacing, or etc...the only thing I noted was with xmgrace theirs a or something at the end, but putting even this in manually to the files did not work...dont know if that helps... Stephan *Gesendet:* Dienstag, 25. Juni 2013 um 10:48 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Can't read 1048576 bytes of 'pullx500.xvg' to compute checksum. Dear Users, I know this error has been discussed many times but the outcome from mdrun -pf and -px stopped at the same time which is 39470 ps. Somehow gromacs caanot read pullx500.xvg but no clue why. I tried dos2gmx and still the same error occur. As I do not care about pullx500.xvg I run grompp again to change the tpr file and set pull_nstxout = 0 then run from the checkpoint but then the error occurs that 4 out of 5 files to append are only present. Can you advise please? Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Quartic angle potential - how to use?
On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann s.neuman...@gmail.com wrote: On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 5:16 AM, Steven Neumann wrote: Thank you. Do you know whether it is possible to use the 5th order polynomial for angles in Gromacs? I know I can use tables but wish to fit my data into such a function. Nothing in the manual seems to suggest that such a form is supported. -Justin Would that be difficult to implement it into the code? Not really, but since you can use a table to describe the functional form even for a bonded interaction (see manual) then you should do that. It's much better to prove the functional form is useful and works when you haven't touched the C code, and only touch the C code when it is clear that performance is an issue (which it probably isn't for any bonded interaction). Mark Thank you. I am trying to avoid tabulated potentials as much as I can so hence my question. Can you please write me where in Gromacs direcotry I could possibly modify it to see the code? Steven On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/5/13 8:40 AM, Steven Neumann wrote: Dear Gmx Users, I wish to use quartic angle potential and specify all constants. I know it is a function 6 of [ angles ] but do not know how to place my polynomial constants? As table 5.5 in the manual indicates, list the equilibrium angle followed by all of the constants, in order. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Quartic angle potential - how to use?
I will speak to someone who is familiar with the code. However, my Gromacs version is installed on the cluster, can I create a file in my directory which will use this code with a given potential? On Wed, Jun 19, 2013 at 8:41 AM, Steven Neumann s.neuman...@gmail.comwrote: On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann s.neuman...@gmail.com wrote: On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 5:16 AM, Steven Neumann wrote: Thank you. Do you know whether it is possible to use the 5th order polynomial for angles in Gromacs? I know I can use tables but wish to fit my data into such a function. Nothing in the manual seems to suggest that such a form is supported. -Justin Would that be difficult to implement it into the code? Not really, but since you can use a table to describe the functional form even for a bonded interaction (see manual) then you should do that. It's much better to prove the functional form is useful and works when you haven't touched the C code, and only touch the C code when it is clear that performance is an issue (which it probably isn't for any bonded interaction). Mark Thank you. I am trying to avoid tabulated potentials as much as I can so hence my question. Can you please write me where in Gromacs direcotry I could possibly modify it to see the code? Steven On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/5/13 8:40 AM, Steven Neumann wrote: Dear Gmx Users, I wish to use quartic angle potential and specify all constants. I know it is a function 6 of [ angles ] but do not know how to place my polynomial constants? As table 5.5 in the manual indicates, list the equilibrium angle followed by all of the constants, in order. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send
Re: [gmx-users] Quartic angle potential - how to use?
Why? To avoid refining and extrapolating 100 tables for a Coarse grained run and use constants instead... And to make it faster obviously. On Wed, Jun 19, 2013 at 9:22 AM, Mark Abraham mark.j.abra...@gmail.comwrote: No. You're modifying the C code, so you will have to learn to maintain a GROMACS installation. Yet another reason to avoid modifying the C code :-) Mark On Wed, Jun 19, 2013 at 10:06 AM, Steven Neumann s.neuman...@gmail.com wrote: I will speak to someone who is familiar with the code. However, my Gromacs version is installed on the cluster, can I create a file in my directory which will use this code with a given potential? On Wed, Jun 19, 2013 at 8:41 AM, Steven Neumann s.neuman...@gmail.com wrote: On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann s.neuman...@gmail.com wrote: On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 5:16 AM, Steven Neumann wrote: Thank you. Do you know whether it is possible to use the 5th order polynomial for angles in Gromacs? I know I can use tables but wish to fit my data into such a function. Nothing in the manual seems to suggest that such a form is supported. -Justin Would that be difficult to implement it into the code? Not really, but since you can use a table to describe the functional form even for a bonded interaction (see manual) then you should do that. It's much better to prove the functional form is useful and works when you haven't touched the C code, and only touch the C code when it is clear that performance is an issue (which it probably isn't for any bonded interaction). Mark Thank you. I am trying to avoid tabulated potentials as much as I can so hence my question. Can you please write me where in Gromacs direcotry I could possibly modify it to see the code? Steven On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/5/13 8:40 AM, Steven Neumann wrote: Dear Gmx Users, I wish to use quartic angle potential and specify all constants. I know it is a function 6 of [ angles ] but do not know how to place my polynomial constants? As table 5.5 in the manual indicates, list the equilibrium angle followed by all of the constants, in order. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http
Re: [gmx-users] Quartic angle potential - how to use?
On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 5:16 AM, Steven Neumann wrote: Thank you. Do you know whether it is possible to use the 5th order polynomial for angles in Gromacs? I know I can use tables but wish to fit my data into such a function. Nothing in the manual seems to suggest that such a form is supported. -Justin Would that be difficult to implement it into the code? On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/5/13 8:40 AM, Steven Neumann wrote: Dear Gmx Users, I wish to use quartic angle potential and specify all constants. I know it is a function 6 of [ angles ] but do not know how to place my polynomial constants? As table 5.5 in the manual indicates, list the equilibrium angle followed by all of the constants, in order. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Quartic Angle
The constant angle has a weird units of kJ /mol rad^n while the angle is in degrees. Does not make sense but at least I know where I made a mistake... On Wed, Jun 12, 2013 at 10:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 10:01 AM, Steven Neumann wrote: Dear Gmx Users, I run a simulation with quartic angle potential. These function has two minima at 100 at 120 degrees. However, seems from my simulation that it is not applied... all angles are around 180 degrees and my chain is a line chain (straight). I have in my topology [ angles ] ; i j k funct th0 C0 C1 C2 C3 C4 123601389.5-46.90530.59033 -0.00328291 0.0680894 in the log file the quartic potential is shown every time. Can it be the reason of th0 to be zero? That's what I'd suspect. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] [ defaults ] and nonbonded
Whether it would be that easy i will find it. I specified my own potential (not LJ) - so how come I should choose option 1 or 2 in nbfunct? I changed h(x) in my table 6th column. On Wed, Jun 12, 2013 at 1:18 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/11/13 4:12 PM, Steven Neumann wrote: Dear Gromacs Users, I got really confused: In manual [defualts ]: nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2 (Buckingham) I want to use mdrun -table table.xvg with my own potential, which one I should choose? gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4 parameters from the pairtypes list. When parameters are not present in the list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters that are not present in the pair list from normal Lennard-Jones parameters using fudgeLJ I want to have all intramolecular atoms (within my chain) interacting (no exclusions) with each other from [ atomtypes ] in ffnonbonded.itp Does it mean yes with nrexcl =1 in my topology? And sth I also got confused: [ pairtypes ] are only 1-4 parameters or here I can specify parameters for all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also correspond to intra molecular interactions? These topics are discussed frequently. Please search the archive; surely you will find relevant topics. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Nonbonded parameters
Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type [ nonbond_params ] these are nonbonded parameters between atoms of different type [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nonbonded parameters
Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nonbonded parameters
On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nonbonded parameters
I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.comwrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un
Re: [gmx-users] Nonbonded parameters
An why do I have 1830 non bonded? 60*60/2 = 1800. There are 57 of 1-4 combinations so it should be lower than 1800... And why 1830 1-4 interactions as I have only 57... Please, help/ Steven On Wed, Jun 12, 2013 at 11:40 AM, Steven Neumann s.neuman...@gmail.comwrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.comwrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users
Re: [gmx-users] Nonbonded parameters
All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] Nonbonded parameters
and 1830 1-4 interactions... there are 57 all possible 1-4 interactions On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.comwrote: All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp
Re: [gmx-users] Nonbonded parameters
60 types of atoms and 60 atoms in total belonging to one residue On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham mark.j.abra...@gmail.comwrote: How many atom *types* are there? On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann s.neuman...@gmail.com wrote: and 1830 1-4 interactions... there are 57 all possible 1-4 interactions On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.com wrote: All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force
Re: [gmx-users] Nonbonded parameters
So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Quartic Angle
Dear Gmx Users, I run a simulation with quartic angle potential. These function has two minima at 100 at 120 degrees. However, seems from my simulation that it is not applied... all angles are around 180 degrees and my chain is a line chain (straight). I have in my topology [ angles ] ; i j k funct th0 C0 C1 C2 C3 C4 123601389.5-46.90530.59033 -0.00328291 0.0680894 in the log file the quartic potential is shown every time. Can it be the reason of th0 to be zero? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Angles not read
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:42 AM, Justin Lemkul wrote: On 6/10/13 8:40 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created: Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will not include a water model Reading 60central_Carbons.pdb... Read 3 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 3 residues with 3 atoms chain #res #atoms 1 'X' 3 3 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./CG.ff/atomtypes.atp Atomtype 1 Reading residue database... (CG) Opening force field file ./CG.ff/aminoacids.rtp Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih 1 1 1 2 0 3 1 1 Residue 13t at the beginning of ./CG.ff/aminoacids.rtp Sorting it all out... Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'X' (3 atoms, 3 residues) Identified residue MET1 as a starting terminus. Identified residue VAL3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms Now there are 3 residues with 3 atoms Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions...There are0 dihedrals,0 impropers,0 angles 0 pairs,0 bonds and 0 virtual sites Total mass 319.420 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.2# Writing coordinate file... Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2# - PLEASE NOTE You have successfully generated a topology from:3Carbons.pdb. The CG force field is used. - ETON ESAELP gcq#304: Gabba Gabba Hey! (The Ramones) It stated that there are no angles. However in my ffbonded.itp which i ncluded in my forcefield.itp [ angletypes ] ; i j k funct th0 C0 C1 C2 C3 C4 CMECSECVA600.0680894-0.0328291000590330 -46.313 How Gromacs can read this angle? [angletypes] simply define possible interactions, but are not used unless there are [angles] in the .rtp that use them. pdb2gmx writes angles based on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot write any angles. Does your .rtp entry specify [angles] but no [bonds]? I want to use constraints with SHAKE as bonds...no harmonic bonds. In this case pdb2gmx will never create angles? Shall I also manually add [ angles ] to my top then? Yes, because in the absence of bonds, even [angles] in .rtp entries are ignored. Thinking a bit more though, it's probably a lot easier to define bonds and let pdb2gmx do the work for you. Using: constraints = all-bonds constraint-algorithm = shake will turn all bonds in the topology into constraints, which sounds like exactly what you want to do. -Justin I want my atoms to be constrained. I specified in my topology [ constraints ] 1 2 0.4 2 3 0.4 etc. Shall use? constraints = none constraint-algorithm = shake I do not have [ bonds ] in my topology -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support
[gmx-users] Constraints of distance
Dear Gmx Users, I am running CG simulation and I wish my beads to be constraint - one away from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not have any bonds in my topology or rtp entry. I just add: [ constraints ] 1 2 1 0.4 2 3 1 0.4 ... 31 32 1 0.4 constraints = none constraint_algorithm = Lincs Is that correct? I used function 1, is that right? Shall I specify something else? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Constraints of distance
I was not sure about the fucntion type (1 or 2). Once in manual it is stated that function 1 is only for exclusions and another time it can be used to miimc bonds. Both functions are working though. Thanks anyway. Steven On Tue, Jun 11, 2013 at 2:18 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: I think all is correct. Why are you asking? People normally report problems. Dr. Vitaly Chaban On Tue, Jun 11, 2013 at 12:30 PM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, I am running CG simulation and I wish my beads to be constraint - one away from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not have any bonds in my topology or rtp entry. I just add: [ constraints ] 1 2 1 0.4 2 3 1 0.4 ... 31 32 1 0.4 constraints = none constraint_algorithm = Lincs Is that correct? I used function 1, is that right? Shall I specify something else? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Constraints of distance
Thank you Justin. So using nrexcl 0 or 1 (should be the same with constraints) and type 1 will allow bonded atoms to interact (vdW) with each other? On Tue, Jun 11, 2013 at 6:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/11/13 10:46 AM, Steven Neumann wrote: I was not sure about the fucntion type (1 or 2). Once in manual it is stated that function 1 is only for exclusions and another time it can be used to miimc bonds. Both functions are working though. Thanks anyway. More precisely, constraints of type 1 generate exclusions between bonded atoms within nrexcl (defined in the topology), whereas type 2 do not. Whether or not you need the constraints to do this depends on the nature of the force field. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] [ defaults ] and nonbonded
Dear Gromacs Users, I got really confused: In manual [defualts ]: nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2 (Buckingham) I want to use mdrun -table table.xvg with my own potential, which one I should choose? gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4 parameters from the pairtypes list. When parameters are not present in the list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters that are not present in the pair list from normal Lennard-Jones parameters using fudgeLJ I want to have all intramolecular atoms (within my chain) interacting (no exclusions) with each other from [ atomtypes ] in ffnonbonded.itp Does it mean yes with nrexcl =1 in my topology? And sth I also got confused: [ pairtypes ] are only 1-4 parameters or here I can specify parameters for all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also correspond to intra molecular interactions? Thank you Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Quartic angle potential - how to use?
Thank you. Do you know whether it is possible to use the 5th order polynomial for angles in Gromacs? I know I can use tables but wish to fit my data into such a function. Steven On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/5/13 8:40 AM, Steven Neumann wrote: Dear Gmx Users, I wish to use quartic angle potential and specify all constants. I know it is a function 6 of [ angles ] but do not know how to place my polynomial constants? As table 5.5 in the manual indicates, list the equilibrium angle followed by all of the constants, in order. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Angles not read
Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created: Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will not include a water model Reading 60central_Carbons.pdb... Read 3 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 3 residues with 3 atoms chain #res #atoms 1 'X' 3 3 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./CG.ff/atomtypes.atp Atomtype 1 Reading residue database... (CG) Opening force field file ./CG.ff/aminoacids.rtp Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih 1 1 1 2 0 3 1 1 Residue 13t at the beginning of ./CG.ff/aminoacids.rtp Sorting it all out... Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'X' (3 atoms, 3 residues) Identified residue MET1 as a starting terminus. Identified residue VAL3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms Now there are 3 residues with 3 atoms Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions...There are0 dihedrals,0 impropers,0 angles 0 pairs,0 bonds and 0 virtual sites Total mass 319.420 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.2# Writing coordinate file... Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2# - PLEASE NOTE You have successfully generated a topology from:3Carbons.pdb. The CG force field is used. - ETON ESAELP gcq#304: Gabba Gabba Hey! (The Ramones) It stated that there are no angles. However in my ffbonded.itp which i ncluded in my forcefield.itp [ angletypes ] ; i j k funct th0 C0 C1 C2 C3 C4 CMECSECVA600.0680894-0.0328291000590330 -46.313 How Gromacs can read this angle? In terms of bonds I want to use constraints, can I use in my ffbonded.itp [ costrainttypes] or add them automatically after? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Angles not read
On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created: Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will not include a water model Reading 60central_Carbons.pdb... Read 3 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 3 residues with 3 atoms chain #res #atoms 1 'X' 3 3 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./CG.ff/atomtypes.atp Atomtype 1 Reading residue database... (CG) Opening force field file ./CG.ff/aminoacids.rtp Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih 1 1 1 2 0 3 1 1 Residue 13t at the beginning of ./CG.ff/aminoacids.rtp Sorting it all out... Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'X' (3 atoms, 3 residues) Identified residue MET1 as a starting terminus. Identified residue VAL3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms Now there are 3 residues with 3 atoms Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions...There are0 dihedrals,0 impropers,0 angles 0 pairs,0 bonds and 0 virtual sites Total mass 319.420 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.2# Writing coordinate file... Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2# - PLEASE NOTE You have successfully generated a topology from:3Carbons.pdb. The CG force field is used. - ETON ESAELP gcq#304: Gabba Gabba Hey! (The Ramones) It stated that there are no angles. However in my ffbonded.itp which i ncluded in my forcefield.itp [ angletypes ] ; i j k funct th0 C0 C1 C2 C3 C4 CMECSECVA600.0680894-0.0328291000590330 -46.313 How Gromacs can read this angle? [angletypes] simply define possible interactions, but are not used unless there are [angles] in the .rtp that use them. pdb2gmx writes angles based on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot write any angles. Does your .rtp entry specify [angles] but no [bonds]? I want to use constraints with SHAKE as bonds...no harmonic bonds. In this case pdb2gmx will never create angles? Shall I also manually add [ angles ] to my top then? In terms of bonds I want to use constraints, can I use in my ffbonded.itp [ costrainttypes] or add them automatically after? You would need [constraints] in your .top file, not [constrainttypes] (same hierarchy as described above with angles). Usually .mdp keywords serve better than topology modifications in the case of constraints, unless you're only constraining a subset of atoms within a single [moleculetype]. I can manually add [ constraints ] to my top after processing with pdb2gmx -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Angles not read
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:42 AM, Justin Lemkul wrote: On 6/10/13 8:40 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created: Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will not include a water model Reading 60central_Carbons.pdb... Read 3 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 3 residues with 3 atoms chain #res #atoms 1 'X' 3 3 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./CG.ff/atomtypes.atp Atomtype 1 Reading residue database... (CG) Opening force field file ./CG.ff/aminoacids.rtp Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih 1 1 1 2 0 3 1 1 Residue 13t at the beginning of ./CG.ff/aminoacids.rtp Sorting it all out... Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'X' (3 atoms, 3 residues) Identified residue MET1 as a starting terminus. Identified residue VAL3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms Now there are 3 residues with 3 atoms Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions...There are0 dihedrals,0 impropers,0 angles 0 pairs,0 bonds and 0 virtual sites Total mass 319.420 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.2# Writing coordinate file... Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2# - PLEASE NOTE You have successfully generated a topology from:3Carbons.pdb. The CG force field is used. - ETON ESAELP gcq#304: Gabba Gabba Hey! (The Ramones) It stated that there are no angles. However in my ffbonded.itp which i ncluded in my forcefield.itp [ angletypes ] ; i j k funct th0 C0 C1 C2 C3 C4 CMECSECVA600.0680894-0.0328291000590330 -46.313 How Gromacs can read this angle? [angletypes] simply define possible interactions, but are not used unless there are [angles] in the .rtp that use them. pdb2gmx writes angles based on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot write any angles. Does your .rtp entry specify [angles] but no [bonds]? I want to use constraints with SHAKE as bonds...no harmonic bonds. In this case pdb2gmx will never create angles? Shall I also manually add [ angles ] to my top then? Yes, because in the absence of bonds, even [angles] in .rtp entries are ignored. Thinking a bit more though, it's probably a lot easier to define bonds and let pdb2gmx do the work for you. Using: constraints = all-bonds constraint-algorithm = shake will turn all bonds in the topology into constraints, which sounds like exactly what you want to do. -Justin Thank you. But specifying [ bonds ] in my rtp file without force constant? Shall i remove [ bonds ] from my top file then? -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Angles not read
On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:53 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:42 AM, Justin Lemkul wrote: On 6/10/13 8:40 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created: Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will not include a water model Reading 60central_Carbons.pdb... Read 3 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 3 residues with 3 atoms chain #res #atoms 1 'X' 3 3 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./CG.ff/atomtypes.atp Atomtype 1 Reading residue database... (CG) Opening force field file ./CG.ff/aminoacids.rtp Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih 1 1 1 2 0 3 1 1 Residue 13t at the beginning of ./CG.ff/aminoacids.rtp Sorting it all out... Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'X' (3 atoms, 3 residues) Identified residue MET1 as a starting terminus. Identified residue VAL3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms Now there are 3 residues with 3 atoms Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions...There are0 dihedrals,0 impropers,0 angles 0 pairs,0 bonds and 0 virtual sites Total mass 319.420 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.2# Writing coordinate file... Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2# - PLEASE NOTE You have successfully generated a topology from:3Carbons.pdb. The CG force field is used. - ETON ESAELP gcq#304: Gabba Gabba Hey! (The Ramones) It stated that there are no angles. However in my ffbonded.itp which i ncluded in my forcefield.itp [ angletypes ] ; i j k funct th0 C0 C1 C2 C3 C4 CMECSECVA600.0680894-0.0328291000590330 -46.313 How Gromacs can read this angle? [angletypes] simply define possible interactions, but are not used unless there are [angles] in the .rtp that use them. pdb2gmx writes angles based on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot write any angles. Does your .rtp entry specify [angles] but no [bonds]? I want to use constraints with SHAKE as bonds...no harmonic bonds. In this case pdb2gmx will never create angles? Shall I also manually add [ angles ] to my top then? Yes, because in the absence of bonds, even [angles] in .rtp entries are ignored. Thinking a bit more though, it's probably a lot easier to define bonds and let pdb2gmx do the work for you. Using: constraints = all-bonds constraint-algorithm = shake will turn all bonds in the topology into constraints, which sounds like exactly what you want to do. -Justin Thank you. But specifying [ bonds ] in my rtp file without force constant? Entries need to be syntactically correct, but the force constant is completely irrelevant if you are constraining all bonds. Shall i remove [ bonds ] from my top file then? What? Without [bonds], you can't do what I'm suggesting. If you don't have [bonds], you have to write [constraints] and [angles] (and any other bonded directories) manually. I am saying about removing them from top after pdb2gmx just to bring [ angles ] to top - I do not want to have a harmonic or any potential for bonds. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] Angles not read
Thank you Justing. Last question - each of my amino acid is one bead. How can I specify [angles ] between atoms corresponding to different residues? Shall I add it at the end of my rtp entry with all amino acids? On Mon, Jun 10, 2013 at 2:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 9:04 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:53 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:42 AM, Justin Lemkul wrote: On 6/10/13 8:40 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created: Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will not include a water model Reading 60central_Carbons.pdb... Read 3 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 3 residues with 3 atoms chain #res #atoms 1 'X' 3 3 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./CG.ff/atomtypes.atp Atomtype 1 Reading residue database... (CG) Opening force field file ./CG.ff/aminoacids.rtp Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih 1 1 1 2 0 3 1 1 Residue 13t at the beginning of ./CG.ff/aminoacids.rtp Sorting it all out... Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'X' (3 atoms, 3 residues) Identified residue MET1 as a starting terminus. Identified residue VAL3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms Now there are 3 residues with 3 atoms Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions...There are0 dihedrals,0 impropers, 0 angles 0 pairs,0 bonds and 0 virtual sites Total mass 319.420 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.2# Writing coordinate file... Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2# - PLEASE NOTE You have successfully generated a topology from:3Carbons.pdb. The CG force field is used. - ETON ESAELP gcq#304: Gabba Gabba Hey! (The Ramones) It stated that there are no angles. However in my ffbonded.itp which i ncluded in my forcefield.itp [ angletypes ] ; i j k funct th0 C0 C1 C2 C3 C4 CMECSECVA600.0680894-0.0328291000590330 -46.313 How Gromacs can read this angle? [angletypes] simply define possible interactions, but are not used unless there are [angles] in the .rtp that use them. pdb2gmx writes angles based on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot write any angles. Does your .rtp entry specify [angles] but no [bonds]? I want to use constraints with SHAKE as bonds...no harmonic bonds. In this case pdb2gmx will never create angles? Shall I also manually add [ angles ] to my top then? Yes, because in the absence of bonds, even [angles] in .rtp entries are ignored. Thinking a bit more though, it's probably a lot easier to define bonds and let pdb2gmx do the work for you. Using: constraints = all-bonds constraint-algorithm = shake will turn all bonds in the topology into constraints, which sounds like exactly what you want to do. -Justin Thank you. But specifying [ bonds ] in my rtp file without force constant? Entries need to be syntactically correct, but the force constant is completely irrelevant if you are constraining all bonds. Shall i remove [ bonds ] from my top file then? What? Without [bonds], you can't do what I'm suggesting. If you don't have [bonds], you have to write [constraints] and [angles] (and any other bonded directories) manually. I am saying about removing them from top after pdb2gmx just to bring [ angles ] to top - I do not want to have a harmonic or any potential for bonds. I suppose you can do that, but why bother? If you want to constrain all bonds with SHAKE, see above. There will be no harmonic potential anywhere if all bonds are constrained. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http
Re: [gmx-users] Angles not read
On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 9:11 AM, Steven Neumann wrote: Thank you Justing. Last question - each of my amino acid is one bead. How can I specify [angles ] between atoms corresponding to different residues? Shall I add it at the end of my rtp entry with all amino acids? Each .rtp entry should only contain one bead, right? The only way to define angles for such a system is to use +/- prefixes for succeeding and preceding residues (beads). -Justin Yes, indeed. Can you provide me the example of such +/-? On Mon, Jun 10, 2013 at 2:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 9:04 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:53 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:42 AM, Justin Lemkul wrote: On 6/10/13 8:40 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created: Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will not include a water model Reading 60central_Carbons.pdb... Read 3 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 3 residues with 3 atoms chain #res #atoms 1 'X' 3 3 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./CG.ff/atomtypes.atp Atomtype 1 Reading residue database... (CG) Opening force field file ./CG.ff/aminoacids.rtp Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih 1 1 1 2 0 3 1 1 Residue 13t at the beginning of ./CG.ff/aminoacids.rtp Sorting it all out... Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'X' (3 atoms, 3 residues) Identified residue MET1 as a starting terminus. Identified residue VAL3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms Now there are 3 residues with 3 atoms Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions...There are0 dihedrals,0 impropers, 0 angles 0 pairs,0 bonds and 0 virtual sites Total mass 319.420 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.2# Writing coordinate file... Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2# - PLEASE NOTE You have successfully generated a topology from:3Carbons.pdb. The CG force field is used. - ETON ESAELP gcq#304: Gabba Gabba Hey! (The Ramones) It stated that there are no angles. However in my ffbonded.itp which i ncluded in my forcefield.itp [ angletypes ] ; i j k funct th0 C0 C1 C2 C3 C4 CMECSECVA600.0680894-0.0328291000 590330 -46.313 How Gromacs can read this angle? [angletypes] simply define possible interactions, but are not used unless there are [angles] in the .rtp that use them. pdb2gmx writes angles based on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot write any angles. Does your .rtp entry specify [angles] but no [bonds]? I want to use constraints with SHAKE as bonds...no harmonic bonds. In this case pdb2gmx will never create angles? Shall I also manually add [ angles ] to my top then? Yes, because in the absence of bonds, even [angles] in .rtp entries are ignored. Thinking a bit more though, it's probably a lot easier to define bonds and let pdb2gmx do the work for you. Using: constraints = all-bonds constraint-algorithm = shake will turn all bonds in the topology into constraints, which sounds like exactly what you want to do. -Justin Thank you. But specifying [ bonds ] in my rtp file without force constant? Entries need to be syntactically correct, but the force constant is completely irrelevant if you are constraining all bonds. Shall i remove [ bonds ] from my top file then? What? Without [bonds], you can't do what I'm suggesting. If you don't have [bonds], you have to write [constraints] and [angles] (and any other bonded directories) manually. I am saying about removing them from top after pdb2gmx just to bring [ angles ] to top - I do not want to have a harmonic or any potential
Re: [gmx-users] Angles not read
On Mon, Jun 10, 2013 at 2:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 9:22 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 9:11 AM, Steven Neumann wrote: Thank you Justing. Last question - each of my amino acid is one bead. How can I specify [angles ] between atoms corresponding to different residues? Shall I add it at the end of my rtp entry with all amino acids? Each .rtp entry should only contain one bead, right? The only way to define angles for such a system is to use +/- prefixes for succeeding and preceding residues (beads). -Justin Yes, indeed. Can you provide me the example of such +/-? Look in any .rtp file that comes with Gromacs. In your case, it is even easier than an atomistic force field. -Justin Obviously... sorry for this question. Thank you. Steven On Mon, Jun 10, 2013 at 2:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 9:04 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:53 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:42 AM, Justin Lemkul wrote: On 6/10/13 8:40 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created: Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will not include a water model Reading 60central_Carbons.pdb... Read 3 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 3 residues with 3 atoms chain #res #atoms 1 'X' 3 3 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./CG.ff/atomtypes.atp Atomtype 1 Reading residue database... (CG) Opening force field file ./CG.ff/aminoacids.rtp Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih 1 1 1 2 0 3 1 1 Residue 13t at the beginning of ./CG.ff/aminoacids.rtp Sorting it all out... Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'X' (3 atoms, 3 residues) Identified residue MET1 as a starting terminus. Identified residue VAL3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms Now there are 3 residues with 3 atoms Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions...There are0 dihedrals,0 impropers, 0 angles 0 pairs,0 bonds and 0 virtual sites Total mass 319.420 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.2# Writing coordinate file... Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2# - PLEASE NOTE You have successfully generated a topology from:3Carbons.pdb. The CG force field is used. - ETON ESAELP gcq#304: Gabba Gabba Hey! (The Ramones) It stated that there are no angles. However in my ffbonded.itp which i ncluded in my forcefield.itp [ angletypes ] ; i j k funct th0 C0 C1 C2 C3 C4 CMECSECVA600.0680894-0.0328291000 590330 -46.313 How Gromacs can read this angle? [angletypes] simply define possible interactions, but are not used unless there are [angles] in the .rtp that use them. pdb2gmx writes angles based on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot write any angles. Does your .rtp entry specify [angles] but no [bonds]? I want to use constraints with SHAKE as bonds...no harmonic bonds. In this case pdb2gmx will never create angles? Shall I also manually add [ angles ] to my top then? Yes, because in the absence of bonds, even [angles] in .rtp entries are ignored. Thinking a bit more though, it's probably a lot easier to define bonds and let pdb2gmx do the work for you. Using: constraints = all-bonds constraint-algorithm = shake will turn all bonds in the topology into constraints, which sounds like exactly what you want to do. -Justin Thank you. But specifying [ bonds ] in my rtp file without force constant? Entries need to be syntactically correct, but the force constant is completely irrelevant if you are constraining all bonds. Shall i remove [ bonds
[gmx-users] User-define non bonded table
Dear Gmx Users,
I want to specify a table to mdrun for non bonded parameters. I wish to set
it up for all atoms with same potential. Is there any example of the table
like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
How can I tell gromacs to use it for all interactions?
Thanks
Steven
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] User-define non bonded table
Thank you, just getting into this. I just dont understand why they start
from x=0.04? Why not 0.02 or sth else?
Steven
On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena
maruthi.s...@gmail.comwrote:
Hi Neumann,
You can use tabulated potential option in
gromacs. Please check the site given below:
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
Thanks,
Mohan
On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Gmx Users,
I want to specify a table to mdrun for non bonded parameters. I wish to
set
it up for all atoms with same potential. Is there any example of the
table
like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
How can I tell gromacs to use it for all interactions?
Thanks
Steven
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] User-define non bonded table
Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x) and
it is written that I need to setup parameters C6 and C12. But where I
should specify them? In :
[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06
or
[ nonbond_params ]
; i j func V(c6) W(c12)
O O 1 0.22617E-02 0.74158E-06
O OA 1 0.22617E-02 0.13807E-05
Or maybe both?
On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/7/13 7:36 AM, Steven Neumann wrote:
Thank you, just getting into this. I just dont understand why they start
from x=0.04? Why not 0.02 or sth else?
You can start the table from whatever value of x that you like, but at a
certain point, it is unlikely that particles ever come that close, given
normal repulsive potentials.
-Justin
On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena
maruthi.s...@gmail.comwrote:
Hi Neumann,
You can use tabulated potential option in
gromacs. Please check the site given below:
http://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentialshttp://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
Thanks,
Mohan
On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Gmx Users,
I want to specify a table to mdrun for non bonded parameters. I wish to
set
it up for all atoms with same potential. Is there any example of the
table
like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
How can I tell gromacs to use it for all interactions?
Thanks
Steven
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists
--
==**==
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
==**==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] User-define non bonded table
On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/7/13 8:21 AM, Steven Neumann wrote:
Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x) and
it is written that I need to setup parameters C6 and C12. But where I
should specify them? In :
[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06
or
[ nonbond_params ]
; i j func V(c6) W(c12)
O O 1 0.22617E-02 0.74158E-06
O OA 1 0.22617E-02 0.13807E-05
Or maybe both?
Try the tutorial first and make sure you can replicate it. If you're just
looking to tweak C6 and C12 parameters, there's no need for tabulated
functions at all.
-Justin
I want to change function g(x) to use Chandler Anderson potential so g(x) =
1/r^6 + 1/4sigma^6. Would that be a combination rule 1 with nonbonded
function type 1 in [ defaults ] ? Then in ffnonbonded.itp in [atomtypes]
can I specify my my own C6 C12 ?
On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/7/13 7:36 AM, Steven Neumann wrote:
Thank you, just getting into this. I just dont understand why they start
from x=0.04? Why not 0.02 or sth else?
You can start the table from whatever value of x that you like, but at
a
certain point, it is unlikely that particles ever come that close, given
normal repulsive potentials.
-Justin
On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena
maruthi.s...@gmail.comwrote:
Hi Neumann,
You can use tabulated potential option
in
gromacs. Please check the site given below:
http://www.gromacs.org/Documentation/How-tos/
Tabulated_Potentialshttp://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentials
http://**www.gromacs.org/Documentation/**How-tos/Tabulated_Potentialshttp://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
Thanks,
Mohan
On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Gmx Users,
I want to specify a table to mdrun for non bonded parameters. I wish
to
set
it up for all atoms with same potential. Is there any example of the
table
like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that
right?
How can I tell gromacs to use it for all interactions?
Thanks
Steven
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users
htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Searchhttp://www.gromacs.org/**Support/Mailing_Lists/Search
h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists
http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users
htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Searchhttp://www.gromacs.org/**Support/Mailing_Lists/Search
h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists
http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists
--
====
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
====
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users
htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists
Re: [gmx-users] User-define non bonded table
It is stated in manual that tables must always contain 7 columns with a
meaningful data (i.e. no zeros). must be entered in all columns.
The example of table6-12.xvg involves xeros until 0.04. How come?
I want to cut my potential at some point to zero - can I put zeros or shall
I specify some values so the potential will equal zero?
On Fri, Jun 7, 2013 at 2:17 PM, Steven Neumann s.neuman...@gmail.comwrote:
On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/7/13 8:21 AM, Steven Neumann wrote:
Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x)
and
it is written that I need to setup parameters C6 and C12. But where I
should specify them? In :
[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06
or
[ nonbond_params ]
; i j func V(c6) W(c12)
O O 1 0.22617E-02 0.74158E-06
O OA 1 0.22617E-02 0.13807E-05
Or maybe both?
Try the tutorial first and make sure you can replicate it. If you're
just looking to tweak C6 and C12 parameters, there's no need for tabulated
functions at all.
-Justin
I want to change function g(x) to use Chandler Anderson potential so g(x)
= 1/r^6 + 1/4sigma^6. Would that be a combination rule 1 with nonbonded
function type 1 in [ defaults ] ? Then in ffnonbonded.itp in [atomtypes]
can I specify my my own C6 C12 ?
On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/7/13 7:36 AM, Steven Neumann wrote:
Thank you, just getting into this. I just dont understand why they
start
from x=0.04? Why not 0.02 or sth else?
You can start the table from whatever value of x that you like, but
at a
certain point, it is unlikely that particles ever come that close, given
normal repulsive potentials.
-Justin
On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena
maruthi.s...@gmail.comwrote:
Hi Neumann,
You can use tabulated potential option
in
gromacs. Please check the site given below:
http://www.gromacs.org/Documentation/How-tos/
Tabulated_Potentialshttp://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentials
http://**www.gromacs.org/Documentation/**
How-tos/Tabulated_Potentialshttp://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
Thanks,
Mohan
On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Gmx Users,
I want to specify a table to mdrun for non bonded parameters. I wish
to
set
it up for all atoms with same potential. Is there any example of the
table
like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that
right?
How can I tell gromacs to use it for all interactions?
Thanks
Steven
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users
htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Searchhttp://www.gromacs.org/**Support/Mailing_Lists/Search
h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists
http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users
htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Searchhttp://www.gromacs.org/**Support/Mailing_Lists/Search
h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists
http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists
--
====
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu
[gmx-users] Quartic angle potential - how to use?
Dear Gmx Users, I wish to use quartic angle potential and specify all constants. I know it is a function 6 of [ angles ] but do not know how to place my polynomial constants? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] diherdal psi vs angle teta plot
Dear Gmx Users, I wish to obtain the 2D scatter plot in which I will have my protein Ca-Ca-Ca tetta angle and the psi angle N(i)-CA(i)-C(k)-N(i+1) of the central residue? Would you please help? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CG angle distribution
Dear Gmx Users, I am building coarse-grained model for my protein. I group them int0 5-10 atoms. I wish to reproduce atomistic equilibrium angles as well as the spring constant. Shall I use g_angle -od option and calulate distributions? Then I will use equilibrium th0 as the centre of the gaussian distribution and adjust spring constant to match this curve? Please, advise. Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] FEP of ion binding protein
Dear Gmx Users, I wish to compare binding free energy obtained from US which I have sucsessfully conducted and the one obtained using FEP. Would you suggest any tutorial? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RDF - water and protein
Dear Gmx Users, I run long simulation of my protein with 50 small molecules in water. I calculated the RDF (Protein - Water) using -surf mol and -rdf mol_com. Please, take a look at my plot: http://speedy.sh/tmJbD/rdf-P-W.png Could you please, explain me why the second peak is so high? Shall I use option -nopbc ? How can I obtain the density [kg/m3] versus the distance? I wish to compare it with RDF of Protein-Ligands so wish to use some normalization for them to be comparable - peaks will be visible. Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Illegal instruction (core dumped) - trjconv
Dear Gmx Users, I produced my trajectory using Gromacs 4.6 on GPUs. When I try: trjconv -s md298_gpu.tpr -f md298_gpu.xtc -pbc mol -ur compact -o md298_gpuURcomp.xtc Select a group: 0 Selected 0: 'System' Reading frame 0 time0.000 Precision of md298_gpu.xtc is 0.001 (nm) Using output precision of 0.001 (nm) Back Off! I just backed up md298_gpuURcomp.xtc to ./#md298_gpuURcomp.xtc.2# Illegal instruction (core dumped) Would you advise? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Illegal instruction (core dumped) - trjconv
On Mon, Apr 29, 2013 at 10:11 AM, Steven Neumann s.neuman...@gmail.comwrote: Dear Gmx Users, I produced my trajectory using Gromacs 4.6 on GPUs. When I try: trjconv -s md298_gpu.tpr -f md298_gpu.xtc -pbc mol -ur compact -o md298_gpuURcomp.xtc Select a group: 0 Selected 0: 'System' Reading frame 0 time0.000 Precision of md298_gpu.xtc is 0.001 (nm) Using output precision of 0.001 (nm) Back Off! I just backed up md298_gpuURcomp.xtc to ./#md298_gpuURcomp.xtc.2# Illegal instruction (core dumped) Would you advise? Steven What I found out is that options -pbc mol or -pbc whole does not work and give this error. Any suggestions please? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] SMD - reproducibility
Dear Users, I am running my puling simulations of ligand with constant velocity. First I minimize and equilibrate my system: grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr mdrun -s em.tpr -deffnm em grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr mdrun -s nvt298.tpr -deffnm nvt298 grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p topol.top -o npt298.tpr mdrun -s npt298.tpr -deffnm npt298 Then I run 10 pulling simulations with the same mdp file: grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_1.tpr mpiexec mdrun -s pull_1.tpr -deffnm pull_1 ... grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_10.tpr mpiexec mdrun -s pull_10.tpr -deffnm pull_10 I get 3 different (but similar) profiles (Force vs time) with 10 simulations as some of them produce exactly the same results... In another system with the same methodology I get 10 similar but different profiles. I am wondering why in this case only 3 types are possible... Shall I try grompp without -t npt.cpt ? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: SMD - reproducibility
Thanks for this. I think option 2 is more reasonable. However, still do not know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD simulations... On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier schl...@uni-mainz.dewrote: Think i now understand your question. Forget what i wrote before. I could imagine the the 'grompp -t npt.cpt' part is a problem. If the simulations would be numerical reproducible, one should get the same results. As they are not, the results will differ somewhat (would think the more, the longer you simulate). But two different simulations would be more equal to each other, than two simulations which start with different velocity distributions for the particles. If you're interested in an stochastic analysis of your system (meaning simulations which are not equal - performing many pulling experiments in reality, one would also have many different starting points) you could do two things: 1) Run a look npt simulation, and use different frames to start the SMD simulations. From each frame the particles should have a different velocity distribution and the results of the SMD simulations should also differ. (Depending on how many SMD simulations you want to perform, this might get expensive, since the starting frame for SMD should be separated by more then a few ps.) 2) Dump the 'npt.cpt' file and randomly determine new velocities for each particle at the start of each SMD simulation. Since each simulation has a different velocity distribution, the SMD simulation wont be the same. This approach has only one weak point. Due to assigning new random velocities you destroy the thermal equilibrium of the system. But if the system was well equilibrated before, this distrubance should only be small and after the first 100-200 ps of the SMD simulaton the system is in thermal equilibrium. If the complete SMD simulation is much longer (couple of ns), the interesting stuff would happen longer after the inital simulation time with the destroyed equilibrium. Hope this helps Thomas Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org: Dear Users, I am running my puling simulations of ligand with constant velocity. First I minimize and equilibrate my system: grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr mdrun -s em.tpr -deffnm em grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr mdrun -s nvt298.tpr -deffnm nvt298 grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p topol.top -o npt298.tpr mdrun -s npt298.tpr -deffnm npt298 Then I run 10 pulling simulations with the same mdp file: grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_1.tpr mpiexec mdrun -s pull_1.tpr -deffnm pull_1 ... grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_10.tpr mpiexec mdrun -s pull_10.tpr -deffnm pull_10 I get 3 different (but similar) profiles (Force vs time) with 10 simulations as some of them produce exactly the same results... In another system with the same methodology I get 10 similar but different profiles. I am wondering why in this case only 3 types are possible... Shall I try grompp without -t npt.cpt ? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Interaction across PBC
Dear Gmx users, My protien has got some strong acidic and strong basic parts. I fold and unfold my protein with different temperaturss. I bserved high affinity of those regions towards each other, they are very close to each other over the simulation. How can I possibly check whether my two regions do not interact across the boundary conditions with such high affinity? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Autocorrelation of C-N
Thanks. Which tool would provide me vectors over a time? Steven On Thu, Apr 18, 2013 at 8:17 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Chapter 8 is your friend. Find a tool to feed data to g_analyze. Mark On Wed, Apr 17, 2013 at 4:23 PM, Steven Neumann s.neuman...@gmail.com wrote: Dear Users, Could you advise me please how to calculate vector C-N autocorrelation function in my protein along the simulation time? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction across PBC
Thank you. Steven On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/23/13 6:37 AM, Steven Neumann wrote: Dear Gmx users, My protien has got some strong acidic and strong basic parts. I fold and unfold my protein with different temperaturss. I bserved high affinity of those regions towards each other, they are very close to each other over the simulation. How can I possibly check whether my two regions do not interact across the boundary conditions with such high affinity? g_mindist -pi with a suitable index group. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction across PBC
Shall I specify one index group for two regions or 2 seprate? g_mindist asks just for one group. would twice as cutoff would be sufficent to assess they do not interact? On Tue, Apr 23, 2013 at 1:54 PM, Steven Neumann s.neuman...@gmail.comwrote: Thank you. Steven On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/23/13 6:37 AM, Steven Neumann wrote: Dear Gmx users, My protien has got some strong acidic and strong basic parts. I fold and unfold my protein with different temperaturss. I bserved high affinity of those regions towards each other, they are very close to each other over the simulation. How can I possibly check whether my two regions do not interact across the boundary conditions with such high affinity? g_mindist -pi with a suitable index group. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] which tool returns vectors?
Dear Users, Does any one know which command is capable to return the vector of a specified group of 2 atoms (e.g. C=O in protein) over the simulation time? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction across PBC
Thanks a lot Steven On Tue, Apr 23, 2013 at 2:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/23/13 9:15 AM, Steven Neumann wrote: Shall I specify one index group for two regions or 2 seprate? g_mindist asks just for one group. If it only takes one, then you can only give it one. would twice as cutoff would be sufficent to assess they do not interact? Probably, maybe less, but that depends on the cutoff itself. Water ordering can persist for up to 2.0 nm or so. -Justin On Tue, Apr 23, 2013 at 1:54 PM, Steven Neumann s.neuman...@gmail.com wrote: Thank you. Steven On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/23/13 6:37 AM, Steven Neumann wrote: Dear Gmx users, My protien has got some strong acidic and strong basic parts. I fold and unfold my protein with different temperaturss. I bserved high affinity of those regions towards each other, they are very close to each other over the simulation. How can I possibly check whether my two regions do not interact across the boundary conditions with such high affinity? g_mindist -pi with a suitable index group. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] run.mdp on 4.6-gpu
Dear Gmx Users, Could you please assess my mdp file on GPUs: title = Protein-ligand complex MD simualation ; Run parameters integrator = md; leap-frog integrator nsteps = 1; 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output ; output coordinates every 25 ps nstvout = 0 ; velocities to output every 25000 steps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1 ; suppress (tlumic) xtc trajectory continuation= yes ; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme= Verlet verlet-buffer-drift = 0.005 ns_type = grid ; search neighboring grid cells nstlist = 20 ; 10 fs vdwtype = cut-off rvdw-switch = 1.0 rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) vdw-modifier = Potential-shift ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted potential rcoulomb ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT coulomb-modifier = Potential-shift ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = System; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 298 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution nstcalclr = 1 ;period between calculations of long-range every step Let me know if you see something wrong please. It seems it works well. Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Autocorrelation of C-N
Dear Users, Could you advise me please how to calculate vector C-N autocorrelation function in my protein along the simulation time? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat set timestep/amb2gmx?
What do you mean by style 8? On Tue, Apr 16, 2013 at 4:51 PM, Mark Abraham mark.j.abra...@gmail.comwrote: See style 8 for trjconv -h Mark On Tue, Apr 16, 2013 at 10:26 AM, francesco oteri francesco.ot...@gmail.com wrote: Hi, yes Marc you are right but the last time I used gromacs on a namd trajectory I noticed that time in the output files is useless 'cause it is always 0. I understand that, since this information is usually took from .trr or .xtc, it cannot be extracted from a .dcd, but it could be more useful using as x the frame number. This could, at least, permitting to visualize the plot with xmgrace without postprocessing the .xvg Francesco 2013/4/16 Mark Abraham mark.j.abra...@gmail.com On Apr 15, 2013 6:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 12:23 PM, Steven Neumann wrote: Dear Gmx Users, I obtained dcd trajectory from simulation in another software. I wish to merge many trajectories using trjcat with a proper timestep. Is that option possible using gromacs or shall use a script to produce tpr file from my prmtop file e.g. amb2gmx ? Any links for such a script? If you linked against VMD libraries when installing, Gromacs can handle any trajectory/coordinate file format that VMD can, thus requiring no conversion. If you need a .tpr file to do the analysis you are trying to do, then yes, you need to convert topology information into the proper format. ...and be aware that a -s option that accepts both .tpr and (say) .gro formats (as shown in g_tool -h) might succeed with the latter if only atom names, rather than (say) bonding connectivity is required for g_tool to work. Mark -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat set timestep/amb2gmx?
I read it... did not know styles are equal to points :) On Wed, Apr 17, 2013 at 4:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/17/13 11:06 AM, Steven Neumann wrote: What do you mean by style 8? Did you read trjconv -h? There's an enumerated list in the very beginning. Mark is pointing you towards #8 in that list. -Justin On Tue, Apr 16, 2013 at 4:51 PM, Mark Abraham mark.j.abra...@gmail.com* *wrote: See style 8 for trjconv -h Mark On Tue, Apr 16, 2013 at 10:26 AM, francesco oteri francesco.ot...@gmail.com wrote: Hi, yes Marc you are right but the last time I used gromacs on a namd trajectory I noticed that time in the output files is useless 'cause it is always 0. I understand that, since this information is usually took from .trr or .xtc, it cannot be extracted from a .dcd, but it could be more useful using as x the frame number. This could, at least, permitting to visualize the plot with xmgrace without postprocessing the .xvg Francesco 2013/4/16 Mark Abraham mark.j.abra...@gmail.com On Apr 15, 2013 6:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 12:23 PM, Steven Neumann wrote: Dear Gmx Users, I obtained dcd trajectory from simulation in another software. I wish to merge many trajectories using trjcat with a proper timestep. Is that option possible using gromacs or shall use a script to produce tpr file from my prmtop file e.g. amb2gmx ? Any links for such a script? If you linked against VMD libraries when installing, Gromacs can handle any trajectory/coordinate file format that VMD can, thus requiring no conversion. If you need a .tpr file to do the analysis you are trying to do, then yes, you need to convert topology information into the proper format. ...and be aware that a -s option that accepts both .tpr and (say) .gro formats (as shown in g_tool -h) might succeed with the latter if only atom names, rather than (say) bonding connectivity is required for g_tool to work. Mark -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] trjcat set timestep/amb2gmx?
Thank you all. Would you suggest any link to a script like amb2gmx.pl ? I cannot fina anything like this - basically I wish to convert top.prmtop to top.tpr. On Tue, Apr 16, 2013 at 9:26 AM, francesco oteri francesco.ot...@gmail.comwrote: Hi, yes Marc you are right but the last time I used gromacs on a namd trajectory I noticed that time in the output files is useless 'cause it is always 0. I understand that, since this information is usually took from .trr or .xtc, it cannot be extracted from a .dcd, but it could be more useful using as x the frame number. This could, at least, permitting to visualize the plot with xmgrace without postprocessing the .xvg Francesco 2013/4/16 Mark Abraham mark.j.abra...@gmail.com On Apr 15, 2013 6:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 12:23 PM, Steven Neumann wrote: Dear Gmx Users, I obtained dcd trajectory from simulation in another software. I wish to merge many trajectories using trjcat with a proper timestep. Is that option possible using gromacs or shall use a script to produce tpr file from my prmtop file e.g. amb2gmx ? Any links for such a script? If you linked against VMD libraries when installing, Gromacs can handle any trajectory/coordinate file format that VMD can, thus requiring no conversion. If you need a .tpr file to do the analysis you are trying to do, then yes, you need to convert topology information into the proper format. ...and be aware that a -s option that accepts both .tpr and (say) .gro formats (as shown in g_tool -h) might succeed with the latter if only atom names, rather than (say) bonding connectivity is required for g_tool to work. Mark -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat set timestep/amb2gmx?
Got this. Thank you On Tue, Apr 16, 2013 at 11:21 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/16/13 5:32 AM, Steven Neumann wrote: Thank you all. Would you suggest any link to a script like amb2gmx.pl ? I cannot fina anything like this - basically I wish to convert top.prmtop to top.tpr. You will not be able to produce a .tpr file directly. The amb2gmx script simply converts the prmtop to a .top file, which can then be input into grompp. -Justin On Tue, Apr 16, 2013 at 9:26 AM, francesco oteri francesco.ot...@gmail.com**wrote: Hi, yes Marc you are right but the last time I used gromacs on a namd trajectory I noticed that time in the output files is useless 'cause it is always 0. I understand that, since this information is usually took from .trr or .xtc, it cannot be extracted from a .dcd, but it could be more useful using as x the frame number. This could, at least, permitting to visualize the plot with xmgrace without postprocessing the .xvg Francesco 2013/4/16 Mark Abraham mark.j.abra...@gmail.com On Apr 15, 2013 6:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 12:23 PM, Steven Neumann wrote: Dear Gmx Users, I obtained dcd trajectory from simulation in another software. I wish to merge many trajectories using trjcat with a proper timestep. Is that option possible using gromacs or shall use a script to produce tpr file from my prmtop file e.g. amb2gmx ? Any links for such a script? If you linked against VMD libraries when installing, Gromacs can handle any trajectory/coordinate file format that VMD can, thus requiring no conversion. If you need a .tpr file to do the analysis you are trying to do, then yes, you need to convert topology information into the proper format. ...and be aware that a -s option that accepts both .tpr and (say) .gro formats (as shown in g_tool -h) might succeed with the latter if only atom names, rather than (say) bonding connectivity is required for g_tool to work. Mark -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support
[gmx-users] Peptide distance matrix
Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? Thank you in advance, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Peptide distance matrix
On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? Steven -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Peptide distance matrix
On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? Steven -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Peptide distance matrix
And another question: I want to analyze all 5 nanoseconds every 20 ns of my trajectory. Would you suggest using trjcat to create one trajectory first and then process to g_mdmat or can I specify time periods (frames) I wish to analyze? Steven On Mon, Apr 15, 2013 at 4:08 PM, Steven Neumann s.neuman...@gmail.com wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? Steven -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Peptide distance matrix
Thank you for this. Steven On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 11:08 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? All C-alpha carbons are in a default index group. Choose it when prompted by g_mdmat and you'll get what you want. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Peptide distance matrix
And last question: Are these minimum distances averaged over the simulation time? Cannot find any equation the way it is calculated... in Manual its written: This minimum distance between two residues Ai and Aj is defined as the smallest distance between any pair of atoms (i 2 Ai, j 2 Aj ). The output is a symmetrical matrix of smallest distances between all residues. And nothing else... Steven On Mon, Apr 15, 2013 at 4:24 PM, Steven Neumann s.neuman...@gmail.comwrote: Thank you for this. Steven On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 11:08 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? All C-alpha carbons are in a default index group. Choose it when prompted by g_mdmat and you'll get what you want. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjcat set timestep/amb2gmx?
Dear Gmx Users, I obtained dcd trajectory from simulation in another software. I wish to merge many trajectories using trjcat with a proper timestep. Is that option possible using gromacs or shall use a script to produce tpr file from my prmtop file e.g. amb2gmx ? Any links for such a script? thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Desired density - genbox
Thanks. So in this case no matter what density I will start with e.g. 480 kg/m3 presuming the force filed is correct I should get at given conditions the density of interest? Steven On Mon, Mar 18, 2013 at 10:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 6:14 PM, Steven Neumann wrote: On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 2:56 PM, Steven Neumann wrote: Dear Gmx Users, I am trying to obtain given density for my system for a given molecule - its a cubic box of 5 nm in dimension. I calculated that I need 850 molecules to get the density of 500 g/mol In my box there is already 1 molecule so I try: genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb Added 819 molecules (out of 849 requested) Output configuration contains 9020 atoms in 820 residues Volume : 125 (nm^3) Density: 480.336 (g/l) Number of SOL molecules: 0 How can I add 30 more molecules using gromacs? I want to avoid adding it manually. Use a larger box and equilibrate. Thanks. Larger box will need more molecules which is quite obvious so the same problem occurs. I need a cubic box first with given fixed density and then equilibrate it. Further step is to extend the box in one dimension to get properties I want. Shall manually add them then? I think you missed the point of what I was saying. You can use a larger box, with 850 molecules inserted, and equilbrate under NPT (using isotropic pressure coupling to guarantee the box stays cubic). Provided the force field model produces the density you want, that's all you need to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Desired density - genbox
On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 2:56 PM, Steven Neumann wrote: Dear Gmx Users, I am trying to obtain given density for my system for a given molecule - its a cubic box of 5 nm in dimension. I calculated that I need 850 molecules to get the density of 500 g/mol In my box there is already 1 molecule so I try: genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb Added 819 molecules (out of 849 requested) Output configuration contains 9020 atoms in 820 residues Volume : 125 (nm^3) Density: 480.336 (g/l) Number of SOL molecules: 0 How can I add 30 more molecules using gromacs? I want to avoid adding it manually. Use a larger box and equilibrate. Thanks. Larger box will need more molecules which is quite obvious so the same problem occurs. I need a cubic box first with given fixed density and then equilibrate it. Further step is to extend the box in one dimension to get properties I want. Shall manually add them then? Steven All genbox tries to do is add molecules randomly, which is not a foolproof process. If the force field parameters indeed produce the correct density, you should be able to produce it rather quickly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Use dihedraltype 4 to allow several multiplicity terms
Thank you all. I found that in my ffbonded.itp I had the same lines with other values. I used the new one produced by the newest version of paramchem blocking the old one. It works now. Steven On Thu, Mar 7, 2013 at 10:24 PM, Baptiste Demoulin bat.demou...@gmail.com wrote: Hello Steven, I would suggest you to look if this angle is not defined somewhere else in your file. Indeed, it seems that the program has another value for this. The 2 and 6 at the end of the line are the multiplicity, so they don't need to be changed. The relevant value is the one indicated in the 'func' column. 9 should be ok, since it describes a function of several Fourier term. I don't understand why grompp propose to chage this to 4... Baptiste 2013/3/7 Steven Neumann s.neuman...@gmail.com Dear Gmx Users, I used charmm server to get the parameters for my new molecule - alkane. i converted it into the gromacs topology. When I try grompp: WARNING 1 [file ffbonded.itp, line 7948]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 0.159787 2 0 0.159787 2 new: CG331 CG321 CG321 CG331 9 0.00 0.1598288 2 WARNING 2 [file ffbonded.itp, line 7949]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 0.159829 2 0 0.159829 2 new: CG331 CG321 CG321 CG331 9 180.00 0.1330512 6 My ffnonbonded.itp corresponding lines: [ dihedraltypes ] ; i j k l funcphi0cp mult CG331 CG321 CG321 CG331 9 0.00 0.1598288 2 CG331 CG321 CG321 CG331 9 180.00 0.1330512 6 Can you please explain me this? Shall use 4 instead of 2 or 6 at the end of these lines? I am using Gromacs 4.5.5 Stevem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Bond potential of atom groups
I have VOTCa already installed. Thank you for this. Steven On Wed, Feb 13, 2013 at 10:34 PM, Broadbent, Richard richard.broadben...@imperial.ac.uk wrote: Dear Steven, There is no universal method to do this and many people spend years studying the various techniques. However, http://pubs.acs.org/doi/abs/10.1021/ct900369w gives an overview of some of the most widespread techniques used and its references will provide further details. Futhermore, the VOTCA code it describes (www.votca.org) provides tools for building such potentials and is compatible with gromacs file formats. Regards, Richard On 13/02/2013 16:07, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, I want to create coarse grained model. I need bond constant and equilibrium distance according to the equation V(r) =K (R - Req)^2 I wish to extract bonded potential between beads made out 3 atoms. I need Req and K. Equilibrium distance is straight forward - g_dist between COM or COG with index file conatining those 3 atoms. To match force constant K I need to extract bonded potential and try to fit to my parabolic curve. My question: How can I get bonded potential between beads of 3 atoms from AA simulation? Do I have to specify energy groups (energgrps) before the run in my mdp and then use g_energy? Thank you Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
