RE: [gmx-users] how to install ngmx
I reckon ngmx is installed by default if you install GROMACS properly. Read the GROMACS manual Appendix D, page 215. And if you really need a better visualisation software you better install some other visualization software like VMD or PyMol. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Devika N T Sent: Thursday, 17 January 2013 6:55 PM To: Discussion list for GROMACS users Subject: [gmx-users] how to install ngmx Hi all Could anyone help me in installing ngmx Thank you * Regards** N.T. Devika* -- 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] separate equilibrium
hi I'm simulating gold nanoparticle interaction with amino acids. I would like first equilibrate the nanoparticle and freeze it. Then I equilibrate protein .Meaning that I want equilibrate them separatelywhile both of them are in one box full of water. And after equilibrium phase I start simulation of them. How can I do this? Fatemeh Ramezani -- 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: Simulation of 2D lattice model
Bogdan, thank you for so detailed explanation. Now it's only intresting to me if it possible to change vdw radius (assuming it as the distance from center of atom to it outer electronic shell)? E.g I want to change such value for each node in my lattice model (e.g for CH2 united atom that value might be 1.5 and I want dicrease it to the 1 A ( as for simple carbon). Might I do it via some simplest modifications in the nonbonded.itp or should I do that by means of changes in sigma/epsillon terms (Which I also must express from A(c6) and B(c12) based on gromac's combination rules) ? James 2013/1/6 Bogdan Costescu bcoste...@gmail.com: On Sun, Jan 6, 2013 at 1:44 PM, James Starlight jmsstarli...@gmail.com wrote: I mean absence of exponential factor in the C6 term :) So to change the vdw radius of the specified atom I should to varry both c6 and c12 shouldn't it ? Hmm, to me these look like very basic force field questions. Did you try to look the Lennard-Jones potential in a good MD book ? Or in the vast amount of resources available for free online ? Or, even better, in the GROMACS manual ? That would take surely less than an hour, while your questions on the subject have stretched over several days. The 6-12 LJ potential is composed of an attractive and repulsive term. The 6-12 combination is often used because of computational efficiency, as the 12-term can be obtained by multiplying the 6-term with itself. Each of these terms has a constant, typically called C6 and C12, which tells how much each term contributes to the total potential. For example, to have only the 6-term, C12 can be set to zero - this is useful when one knows how much attractive and how much repulsive the potential should be. Most often though, one thinks of the LJ potential in terms of equilibrium distance (obtained through a combination rule) and potential well, expressed through the sigma and epsilon constants. The two pairs (C6/C12 and sigma/epsilon) are interrelated. The relation is given in the GROMACS manual, on the Wikipedia page related to the LJ potential and in many other places. GROMACS also comes with a tool (g_sigeps) which allows an easy transformation between them. As you can see from the formulas, sigma depends on both C6 and C12 and epsilon depends on both C6 and C12. So, to partly answer your question, to change the equilibrium distance (sigma) you need to vary both C6 and C12. It's only partly answered because you need to read about combination rules in the GROMACS manual to see how to get from the atom radius to LJ potential sigma... Please note that a particular force field uses only one of the pairs (C6/C12 or sigma/epsilon) - you can't mix and match. If you want to use f.e. OPLS-AA, all LJ interactions are expressed using the sigma/epsilon pair. If you want to introduce in this force field a new type of interaction based on another force field which is defined using the C6/C12 pair, you have to perform the conversion to sigma/epsilon. If, on the other hand, you design your own force field, you are free to use either of the two pairs but, once chosen, you have to be consistent and use that pair for all LJ interactions. Cheers, Bogdan -- 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] dna-ligand simulation
On 1/17/13 1:19 AM, sarah k wrote: Dear all, 1- I’m trying to simulate a DNA-ligand complex. I have to use AMBER force field for the DNA structure. I have used PRODRG to get the required files and parameters of my ligand. PRODRG generates GROMOS based files. Consequently, when I add the ligand to my ligand topology and coordinates to DNA files, Gromacs can’t recognize some atom types in AMBER force field. Can I expect such simulation to give reliable results? How can I solve the problem? No, the result would be nonsense even if you managed to hack the topology into working. Do not mix and match force fields. You will need to find a way to generate ligand parameters that are compatible with the AMBER force field you've chosen (acpype, antechamber, etc). 2- I would like to save my final *.gro file during md simulation step after each 0.5 ns. How can I do so? The simplest way is to set an appropriate value of nstxtcout and use trjconv to extract the frames later. -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
Re: [gmx-users] residuetype.dat file missing
On 1/17/13 1:25 AM, Devika N T wrote: Thank you Emanuel I have followed the path only usr/share/gromacs/top -- but was missing Then I followed /usr/local/gromacs/share/gromacs/top - I could find residuetype.dat Previously I was having gromacs version 4.0.7, now I have installed 4.5.5. So I doubt some problem which removing and installing... If you have multiple versions on a given computer, it is always better to install them in separate (non-default) locations by specifying an installation location during configuration. /usr/local/gromacs is the default install location. If you want to have multiple versions running concurrently (switchable by sourcing the right GMXRC), you could use, for instance /usr/local/gromacs-4.0.7 and /usr/local/gromacs-4.5.5. -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
Re: [gmx-users] separate equilibrium
On 1/17/13 4:41 AM, fatemeh ramezani wrote: hi I'm simulating gold nanoparticle interaction with amino acids. I would like first equilibrate the nanoparticle and freeze it. Then I equilibrate protein .Meaning that I want equilibrate them separatelywhile both of them are in one box full of water. And after equilibrium phase I start simulation of them. How can I do this? Apply freezegrps or position restraints to whatever you want to hold fixed. -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] RE: No default Proper Dih. types
Thank you Justin, but there is still something I do not understand. Could you please help me with it? I believe that with the line -CB CA1 +CB +CA1 gd_34 in aminoacids.rtp I am defining the torsion the program is complaining about. I also tried with a line -CH3 CH1 +CH2 +CH1 gd_34 and I still have the same problem. In fact, CB is of type CH3 (defined in residue MEE) or type CH2 (defined in residue MEM); CA1 of type CH1 (as defined in residue NIP). The torsion parameters are defined by the set gd_34, which can be found at ffbonded.itp: #define gd_34 0.000 5.92 3 ; -CHn,SI-CHn- 1.4 As I see it, the torsion for this set of atoms is properly defined in aminoacids.rtp, and the parameters of the torsion are properly defined in ffbonded.itp, so they should be read without problems by grompp. What am I doing wrong? What must be done to declare this torsion for that set of atoms? I implemented this molecule before using the all-atom OPLS force field without problems. -- View this message in context: http://gromacs.5086.n6.nabble.com/No-default-Proper-Dih-types-tp4442749p5004656.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: No default Proper Dih. types
On 1/17/13 5:40 AM, escajarro wrote: Thank you Justin, but there is still something I do not understand. Could you please help me with it? I believe that with the line -CB CA1 +CB +CA1 gd_34 in aminoacids.rtp I am defining the torsion the program is complaining about. I also tried with a line -CH3 CH1 +CH2 +CH1 gd_34 This won't work, because the .rtp file requires atom names, not types. and I still have the same problem. In fact, CB is of type CH3 (defined in residue MEE) or type CH2 (defined in residue MEM); CA1 of type CH1 (as defined in residue NIP). The torsion parameters are defined by the set gd_34, which can be found at ffbonded.itp: #define gd_34 0.000 5.92 3 ; -CHn,SI-CHn- 1.4 As I see it, the torsion for this set of atoms is properly defined in aminoacids.rtp, and the parameters of the torsion are properly defined in ffbonded.itp, so they should be read without problems by grompp. What am I doing wrong? What must be done to declare this torsion for that set of atoms? I implemented this molecule before using the all-atom OPLS force field without problems. It doesn't work because you're defining a dihedral across 3 residues, and pdb2gmx doesn't have machinery to deal with that. The atoms in question belong to MEA, NIP, MEM, then the next NIP. pdb2gmx can, at most, connect the previous residue (using a - prefix) to the next residue (with + prefix), but there is no option to include a residue that is two residues downstream. Either manually add the gd_34 declaration in the .top or revise the way your residues are set up so that you don't have one-atom residues. -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] RE: No default Proper Dih. types
Thank you! That clarifies it, I will redefine the residues. This definition was good enough for an all-atom force field, but it seems that not for this. -- View this message in context: http://gromacs.5086.n6.nabble.com/No-default-Proper-Dih-types-tp4442749p5004659.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Simulation of 2D lattice model
On Thu, Jan 17, 2013 at 10:59 AM, James Starlight jmsstarli...@gmail.com wrote: thank you for so detailed explanation. You're welcome. Now it's up to you to use it :) Now it's only intresting to me if it possible to change vdw radius (assuming it as the distance from center of atom to it outer electronic shell)? Yes, it's possible. E.g I want to change such value for each node in my lattice model (e.g for CH2 united atom that value might be 1.5 and I want dicrease it to the 1 A ( as for simple carbon). Might I do it via some simplest modifications in the nonbonded.itp or should I do that by means of changes in sigma/epsillon terms (Which I also must express from A(c6) and B(c12) based on gromac's combination rules) ? If nonbonded.itp for your chosen force field is expressed in sigma/epsilon (I guess that this is the case because you talk about an existing value for sigma), then it's only a matter of changing the sigma parameter of that atomic species. Keep in mind that this is only a description of the change - it doesn't guarantee that the change is valid. If I'd be a reviewer I'd ask for a reason for changing one of the parameters (sigma) and keeping the other (epsilon) constant. Cheers, Bogdan -- 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] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format
Dear all, we'd need to convert a trajectory in .xtc format (and the related topology file) to a format that could be read by Amber program (I'd need to perform MM-PBSA calculations). We tried to do it using VMD, but failed to produce a correct trajectory to be read by MMPBSA.py tool. It complains about the fact that it expected only 3 or 6 box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9 box coords. I read the gmx-user archive to find hints to overcome the problem, but only found incomplete, and in some cases quite old, suggestions (We are currently using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on how to proceed, and I have even the doubt that this is not possible to do. Could you please give me some information about, possibly with detailed descriptions about the commands and the flags to use? Many thanks in advance for your kind answer and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format
On 1/17/13 6:22 AM, Anna Marabotti wrote: Dear all, we'd need to convert a trajectory in .xtc format (and the related topology file) to a format that could be read by Amber program (I'd need to perform MM-PBSA calculations). We tried to do it using VMD, but failed to produce a correct trajectory to be read by MMPBSA.py tool. It complains about the fact that it expected only 3 or 6 box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9 box coords. I read the gmx-user archive to find hints to overcome the problem, but only found incomplete, and in some cases quite old, suggestions (We are currently using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on how to proceed, and I have even the doubt that this is not possible to do. Could you please give me some information about, possibly with detailed descriptions about the commands and the flags to use? You can write a new box using trjconv and make it whatever you want. Presumably you're stripping out water and such anyway, so all you would have to do is center your solute in whatever box you want: trjconv -s topol.tpr -f traj.xtc -center -box x y z -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
Re: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format
On Jan 17, 2013, at 12:27 , Justin Lemkul wrote: On 1/17/13 6:22 AM, Anna Marabotti wrote: Dear all, we'd need to convert a trajectory in .xtc format (and the related topology file) to a format that could be read by Amber program (I'd need to perform MM-PBSA calculations). We tried to do it using VMD, but failed to produce a correct trajectory to be read by MMPBSA.py tool. It complains about the fact that it expected only 3 or 6 box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9 box coords. I read the gmx-user archive to find hints to overcome the problem, but only found incomplete, and in some cases quite old, suggestions (We are currently using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on how to proceed, and I have even the doubt that this is not possible to do. Could you please give me some information about, possibly with detailed descriptions about the commands and the flags to use? The magic bullet for converting rhombic dodecahedron box trajectories into something that makes intuitive sense is to use trjconv with the flags -ur compact and -pbc mol. Then trjconv will pick the periodic copy of each molecule that has its mass center the closest to the box center instead of the default of choosing the periodic image that has the mass center inside of the triclinic box. You can write a new box using trjconv and make it whatever you want. Presumably you're stripping out water and such anyway, so all you would have to do is center your solute in whatever box you want: -Justin I agree with Justin. It is probably best to strip of all water and create a new box if amber cannot understand triclinic boxes. Use the -center or the -fit flag if the solute diffuses out from the original periodic copy of the box. (But be wary to use -fit with operations that rotate the box!) I recommend that you save the original trajectory. Daniel -- 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] Movements of secondary structure
Dear all, I have been trying to calculate and plot the secondary structure of helix movements during the simulation on time through g_helix, g_helix orient, g_principle and g_mindist but none of them shown the helix movements. Is there any other tool can elaborate the helix movements ? Plz suggestion are appreciated. -- 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: Simulation of 2D lattice model
Bogdan, thanks againfor explanation. So if I have force field with the C6/C12 terms (instead of sigma\epsilon) I need to express sigma (which correspond to the Rmin in LJ equation) as the (C12/C6)^0.5. Than if I want to increase sigma ( and consequently to increase vdw radius of my atom) I must to increase c12 or decreace C6 terms. Does it correct in general ? 2013/1/17 Bogdan Costescu bcoste...@gmail.com: On Thu, Jan 17, 2013 at 10:59 AM, James Starlight jmsstarli...@gmail.com wrote: thank you for so detailed explanation. You're welcome. Now it's up to you to use it :) Now it's only intresting to me if it possible to change vdw radius (assuming it as the distance from center of atom to it outer electronic shell)? Yes, it's possible. E.g I want to change such value for each node in my lattice model (e.g for CH2 united atom that value might be 1.5 and I want dicrease it to the 1 A ( as for simple carbon). Might I do it via some simplest modifications in the nonbonded.itp or should I do that by means of changes in sigma/epsillon terms (Which I also must express from A(c6) and B(c12) based on gromac's combination rules) ? If nonbonded.itp for your chosen force field is expressed in sigma/epsilon (I guess that this is the case because you talk about an existing value for sigma), then it's only a matter of changing the sigma parameter of that atomic species. Keep in mind that this is only a description of the change - it doesn't guarantee that the change is valid. If I'd be a reviewer I'd ask for a reason for changing one of the parameters (sigma) and keeping the other (epsilon) constant. Cheers, Bogdan -- 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] Movements of secondary structure
On 1/17/13 7:37 AM, 라지브간디 wrote: Dear all, I have been trying to calculate and plot the secondary structure of helix movements during the simulation on time through g_helix, g_helix orient, g_principle and g_mindist but none of them shown the helix movements. Is there any other tool can elaborate the helix movements ? Plz suggestion are appreciated. You'll have to define what you mean by helix movements. Everything moves in a simulation, but what is it that you're trying to quantify? If it's secondary structure itself, use do_dssp. If you're after something else, you will have to be more specific. -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
Re: [gmx-users] Re: Simulation of 2D lattice model
On Thu, Jan 17, 2013 at 1:51 PM, James Starlight jmsstarli...@gmail.com wrote: So if I have force field with the C6/C12 terms (instead of sigma\epsilon) I need to express sigma (which correspond to the Rmin in LJ equation) as the (C12/C6)^0.5. Than if I want to increase sigma ( and consequently to increase vdw radius of my atom) I must to increase c12 or decreace C6 terms. Does it correct in general ? I think that I have already answered the question - please re-read my previous messages in the thread. Cheers, Bogdan -- 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] 60% slowdown with GPU / verlet and sd integrator
Dear Gromacs Developers! Using sd1 integrator I've obtain good performance with the core-5 + GTX 670 ( 13ns\per day) for the system of 60k atoms. That results on 30% better than with the sd integrator. Buit on my another work-station which differs only by slower GPU ( GT 640). I've obtained some gpu\cpu mis-match. Force evaluation time GPU/CPU: 6.835 ms/2.026 ms = 3.373( # on the first station with GTX 670 I ve obtained GPU/CPU: ratio close to 1. At both cases I'm using the same simulation parameters with 0,8 cutoffs (it's also important that in the second case I've calculated another system consisted of 33k atoms by means of umbrella sampling pulling)). Could you tell me how I could increase performance on my second station ( to reduce gpucpu ratio) ? I've attached log for that simulation here http://www.sendspace.com/file/x0e3z8 James 2013/1/17 Szilárd Páll szilard.p...@cbr.su.se: Hi, Just to note for the users who might read this: the report is valid, some non-thread-parallel code is the reason and we hope to have a fix for 4.6.0. For updates, follow the issue #1211. Cheers, -- Szilárd On Wed, Jan 16, 2013 at 4:45 PM, Berk Hess g...@hotmail.com wrote: The issue I'm referring to is about a factor of 2 in update and constraints, but here it's much more. I just found out that the SD update is not OpenMP threaded (and I even noted in the code why this is). I reopened the issue and will find a solution. Cheers. Berk Date: Wed, 16 Jan 2013 16:20:32 +0100 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: mark.j.abra...@gmail.com To: gmx-users@gromacs.org We should probably note this effect on the wiki somewhere? Mark On Wed, Jan 16, 2013 at 3:44 PM, Berk Hess g...@hotmail.com wrote: Hi, Unfortunately this is not a bug, but a feature! We made the non-bondeds so fast on the GPU that integration and constraints take more time. The sd1 integrator is almost as fast as the md integrator, but slightly less accurate. In most cases that's a good solution. I closed the redmine issue: http://redmine.gromacs.org/issues/1121 Cheers, Berk Date: Wed, 16 Jan 2013 17:26:18 +0300 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: jmsstarli...@gmail.com To: gmx-users@gromacs.org Hi all! I've also done some calculations with the SD integraator used as the thermostat ( without t_coupl ) with the system of 65k atoms I obtained 10ns\day performance on gtc 670 and 4th core i5. I haventrun any simulations with MD integrator yet so It should test it. James 2013/1/15 Szilárd Páll szilard.p...@cbr.su.se: Hi Floris, Great feedback, this needs to be looked into. Could you please file a bug report, preferably with a tpr (and/or all inputs) as well as log files. Thanks, -- Szilárd On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens floris_buel...@yahoo.comwrote: Hi, I'm seeing MD simulation running a lot slower with the sd integrator than with md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found no documented indication that this should be the case. Timings and logs pasted in below - wall time seems to be accumulating up in Update and Rest, adding up to 60% of total. The effect is still there without GPU, ca. 40% slowdown when switching from group to Verlet with the SD integrator System: Xeon E5-1620, 1x GTX 680, gromacs 4.6-beta3-dev-20130107-e66851a-unknown, GCC 4.4.6 and 4.7.0 I didn't file a bug report yet as I don't have much variety of testing conditions available right now, I hope someone else has a moment to try to reproduce? Timings: cpu (ns/day) sd / verlet: 6 sd / group: 10 md / verlet: 9.2 md / group: 11.4 gpu (ns/day) sd / verlet: 11 md / verlet: 29.8 **MD integrator, GPU / verlet M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - Pair Search distance check 1244.988096 11204.893 0.1 NxN QSTab Elec. + VdW [F] 194846.615488 7988711.235 91.9 NxN QSTab Elec. + VdW [VF] 2009.923008 118585.457 1.4 1,4 nonbonded interactions 31.616322 2845.469 0.0 Calc Weights 703.010574 25308.381 0.3 Spread Q Bspline 14997.558912 29995.118 0.3 Gather F
Re: [gmx-users] Re: Simulation of 2D lattice model
Bogdan, It's not clear for me how I could change sigma with fixed epsilon in case of using (A/R)^12-(A/R)^6 form of LJ. In that case sigma and epsion depends both on A and B so changing A or B we will influence both sigma and epsilon. James 2013/1/17 Bogdan Costescu bcoste...@gmail.com: On Thu, Jan 17, 2013 at 1:51 PM, James Starlight jmsstarli...@gmail.com wrote: So if I have force field with the C6/C12 terms (instead of sigma\epsilon) I need to express sigma (which correspond to the Rmin in LJ equation) as the (C12/C6)^0.5. Than if I want to increase sigma ( and consequently to increase vdw radius of my atom) I must to increase c12 or decreace C6 terms. Does it correct in general ? I think that I have already answered the question - please re-read my previous messages in the thread. Cheers, Bogdan -- 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] Re: Simulation of 2D lattice model
On 1/17/13 9:51 AM, James Starlight wrote: Bogdan, It's not clear for me how I could change sigma with fixed epsilon in case of using (A/R)^12-(A/R)^6 form of LJ. In that case sigma and epsion depends both on A and B so changing A or B we will influence both sigma and epsilon. From manual section 5.3.2, equation 5.1 (also available on Wikipedia and wherever else you might Google): C6 = 4 * epsilon * sigma^6 C12 = 4 * epsilon * sigma^12 It's therefore very easy to recalculate C6 and C12 simply by altering sigma, not that I advocate for doing so in a general sense. But that's how you'd do it. -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
RE: [gmx-users] 60% slowdown with GPU / verlet and sd integrator
Hi, Please use the fix I put on the redmine issue, as that's even faster and you can use sd again. We should probably rephrase the note a bit in case the GPU has more work to do than the CPU. In your case there is simple no work to do for the CPU. Ideally we would let the CPU handle some non-bonded work, but that probably won't happen in 4.6. A solution might be buying a 3x a fast GPU. Cheers, Berk Date: Thu, 17 Jan 2013 18:48:17 +0400 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: jmsstarli...@gmail.com To: gmx-users@gromacs.org Dear Gromacs Developers! Using sd1 integrator I've obtain good performance with the core-5 + GTX 670 ( 13ns\per day) for the system of 60k atoms. That results on 30% better than with the sd integrator. Buit on my another work-station which differs only by slower GPU ( GT 640). I've obtained some gpu\cpu mis-match. Force evaluation time GPU/CPU: 6.835 ms/2.026 ms = 3.373 ( # on the first station with GTX 670 I ve obtained GPU/CPU: ratio close to 1. At both cases I'm using the same simulation parameters with 0,8 cutoffs (it's also important that in the second case I've calculated another system consisted of 33k atoms by means of umbrella sampling pulling)). Could you tell me how I could increase performance on my second station ( to reduce gpucpu ratio) ? I've attached log for that simulation here http://www.sendspace.com/file/x0e3z8 James 2013/1/17 Szilárd Páll szilard.p...@cbr.su.se: Hi, Just to note for the users who might read this: the report is valid, some non-thread-parallel code is the reason and we hope to have a fix for 4.6.0. For updates, follow the issue #1211. Cheers, -- Szilárd On Wed, Jan 16, 2013 at 4:45 PM, Berk Hess g...@hotmail.com wrote: The issue I'm referring to is about a factor of 2 in update and constraints, but here it's much more. I just found out that the SD update is not OpenMP threaded (and I even noted in the code why this is). I reopened the issue and will find a solution. Cheers. Berk Date: Wed, 16 Jan 2013 16:20:32 +0100 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: mark.j.abra...@gmail.com To: gmx-users@gromacs.org We should probably note this effect on the wiki somewhere? Mark On Wed, Jan 16, 2013 at 3:44 PM, Berk Hess g...@hotmail.com wrote: Hi, Unfortunately this is not a bug, but a feature! We made the non-bondeds so fast on the GPU that integration and constraints take more time. The sd1 integrator is almost as fast as the md integrator, but slightly less accurate. In most cases that's a good solution. I closed the redmine issue: http://redmine.gromacs.org/issues/1121 Cheers, Berk Date: Wed, 16 Jan 2013 17:26:18 +0300 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: jmsstarli...@gmail.com To: gmx-users@gromacs.org Hi all! I've also done some calculations with the SD integraator used as the thermostat ( without t_coupl ) with the system of 65k atoms I obtained 10ns\day performance on gtc 670 and 4th core i5. I haventrun any simulations with MD integrator yet so It should test it. James 2013/1/15 Szilárd Páll szilard.p...@cbr.su.se: Hi Floris, Great feedback, this needs to be looked into. Could you please file a bug report, preferably with a tpr (and/or all inputs) as well as log files. Thanks, -- Szilárd On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens floris_buel...@yahoo.comwrote: Hi, I'm seeing MD simulation running a lot slower with the sd integrator than with md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found no documented indication that this should be the case. Timings and logs pasted in below - wall time seems to be accumulating up in Update and Rest, adding up to 60% of total. The effect is still there without GPU, ca. 40% slowdown when switching from group to Verlet with the SD integrator System: Xeon E5-1620, 1x GTX 680, gromacs 4.6-beta3-dev-20130107-e66851a-unknown, GCC 4.4.6 and 4.7.0 I didn't file a bug report yet as I don't have much variety of testing conditions available right now, I hope someone else has a moment to try to reproduce? Timings: cpu (ns/day) sd / verlet: 6 sd / group: 10 md / verlet: 9.2 md / group: 11.4 gpu (ns/day) sd / verlet: 11 md / verlet: 29.8 **MD integrator, GPU / verlet
Re: [gmx-users] Minimization problem
On 1/17/13 9:54 AM, Marcelo Depolo wrote: Well, Justin, I tried to generate the .tpr using single precision and I got the same warning. I also tried to use gmxcheck using the command line below: *$ gmxcheck -e prt_cg.edr -m cg.tex* Unfortunately, I got the same warning and no log file. What is a I/O issue? You won't get a log file. The -m flag is used only to print methods information from the .tpr file and is not relevant here. An I/O issue is an input/output problem (i.e. reading/writing from/to the disk). If it happens every time you run the minimization, that doesn't sound like it's relevant. Is this reproducible with 4.6beta3? -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] About Grid MAT
Dear Justin Thank you for your Previous Reply Mail I am using GridMAt MD Script When I run the APL Headgroup Calculation It runs well But I Have got Output With the Following Comment in My Command Prompt looking for offending protein atoms... There are 143 protein atoms within the headgroups of the top leaflet There are 65 protein atoms within the headgroups of the bottom leaflet To Avoid this Which Parameter Should I adjust Either precision Parameter or P_value Parameter Thanks In Advance -- 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] About Grid MAT
On 1/17/13 10:56 AM, vidhya sankar wrote: Dear Justin Thank you for your Previous Reply Mail I am using GridMAt MD Script When I run the APL Headgroup Calculation It runs well But I Have got Output With the Following Comment in My Command Prompt looking for offending protein atoms... There are 143 protein atoms within the headgroups of the top leaflet There are 65 protein atoms within the headgroups of the bottom leaflet To Avoid this Which Parameter Should I adjust Either precision Parameter or P_value Parameter This is the correct output. If you are doing an APL calculation in the presence of a protein, that needs to be taken into account. You can send GridMAT-MD questions directly to me rather than spamming the list with non-Gromacs questions. -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] au--protein separate equilibration
1. For separate equilibration of AU and Protein, I'm using this em.mdp file for equilibration in step 1, that Protein and SOL are frozen: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein SOL freezedim = Y Y Y Y Y Y comm_mode = None 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None 3. In simulation, I'm using this md.mdp file: title = Yo cpp = /lib/cpp define = integrator = md tinit = 0.0 dt = 0.002 nsteps = 25 nstxout = 2500 nstvout = 2500 nstlog = 500 nstenergy = 250 nstxtcout = 0 pbc = xyz rlist = 1.00 coulombtype = PME r_coulomb = 1.00 fourierspacing = 0.10 pme_order = 6 ewald_rtol = 1e-6 vdw-type = switch rvdw-switch = 0.90 rvdw = 1.00 tcoupl = nose-hoover tc_grps = SOL AUS AUB AUI tau_t = 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 Pcoupl = no gen_vel = yes gen_temp = 10 gen_seed = 173529 ; GolP has been tested with lincs only constraints = none constraint_algorithm = lincs lincs_order = 4 lincs_iter = 1 lincs_warnangle = 80 freezegrps = AU AUI freezedim = Y Y Y Y Y Y comm_mode = None Are these .mdp file right? Fatemeh Ramezani -- 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: lincs warning during simulatiion of open-to-close transitions
In addition to LINCS warning during last simulation I obtained the next warning from mdrun (again that was when calmodulin reached close compact conformation) WARNING: Listed nonbonded interaction between particles 1230 and 1249 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. what does it mean and how I could avoid it ? 2013/1/17 James Starlight jmsstarli...@gmail.com: Dear Gromacs Users! I'm simulatting open to close transition of calmodulin by means of essential dynamics sampling. When my protein reaches closed state (this time both ef hands domains aproach each other) I've obtain set of lincs warnings and my simulatting crashes. I'm using gpu-based gromacs with the sd integrator (As the thermostat). Below you can see parameters for lincs options 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 Does it possible to resolve such problem by means of modification of lincs options in mdp file ? James -- 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: lincs warning during simulatiion of open-to-close transitions
On 1/17/13 1:24 PM, James Starlight wrote: In addition to LINCS warning during last simulation I obtained the next warning from mdrun (again that was when calmodulin reached close compact conformation) WARNING: Listed nonbonded interaction between particles 1230 and 1249 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. what does it mean and how I could avoid it ? Note the IMPORTANT statement. Your system is blowing up. Whatever you're doing is causing the physical model to fail. -Justin 2013/1/17 James Starlight jmsstarli...@gmail.com: Dear Gromacs Users! I'm simulatting open to close transition of calmodulin by means of essential dynamics sampling. When my protein reaches closed state (this time both ef hands domains aproach each other) I've obtain set of lincs warnings and my simulatting crashes. I'm using gpu-based gromacs with the sd integrator (As the thermostat). Below you can see parameters for lincs options 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 Does it possible to resolve such problem by means of modification of lincs options in mdp file ? James -- 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
Re: [gmx-users] Re: Simulation of 2D lattice model
Justin, so following to that equation the alteration of sigma will affect on both C6 and C12 ( attractive and repuslive terms). I dont quite understand how such modifications of the c6 and c12 params will change vdw radius of atom. I need some example to understand it :( James 2013/1/17 Justin Lemkul jalem...@vt.edu: On 1/17/13 9:51 AM, James Starlight wrote: Bogdan, It's not clear for me how I could change sigma with fixed epsilon in case of using (A/R)^12-(A/R)^6 form of LJ. In that case sigma and epsion depends both on A and B so changing A or B we will influence both sigma and epsilon. From manual section 5.3.2, equation 5.1 (also available on Wikipedia and wherever else you might Google): C6 = 4 * epsilon * sigma^6 C12 = 4 * epsilon * sigma^12 It's therefore very easy to recalculate C6 and C12 simply by altering sigma, not that I advocate for doing so in a general sense. But that's how you'd do it. -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] au--protein separate equilibration
On 1/17/13 12:15 PM, fatemeh ramezani wrote: 1. For separate equilibration of AU and Protein, I'm using this em.mdp file for equilibration in step 1, that Protein and SOL are frozen: This is not an equilibration, this is an energy minimization, which will likely not accomplish much with so many particles frozen. title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb= 1 rvdw= 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein SOL freezedim = Y Y YY Y Y comm_mode = None I suppose this .mdp file will allow whatever the Au particle is to move, but I don't see much point to running anything where the solvent is frozen. Freezing water also makes -DFLEXBILE irrelevant. 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb= 1 rvdw= 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps =AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None 3. In simulation, I'm using this md.mdp file: title= Yo cpp = /lib/cpp define = integrator = md tinit= 0.0 dt = 0.002 nsteps = 25 nstxout = 2500 nstvout = 2500 nstlog = 500 nstenergy= 250 nstxtcout= 0 pbc = xyz rlist= 1.00 coulombtype = PME r_coulomb= 1.00 The correct keyword is rcoulomb. fourierspacing = 0.10 Why switch the fourierspacing here? You used 0.12 before, and now you'r eusing 0.10. pme_order= 6 ewald_rtol = 1e-6 vdw-type = switch rvdw-switch = 0.90 rvdw = 1.00 These vdw settings are all very different from the previous minimization step. It's usually a good idea to keep the settings the same throughout all steps, otherwise you're using some broken form of a force field intermittently. tcoupl = nose-hoover tc_grps = SOL AUS AUB AUI tau_t= 0.1 0.1 0.1 0.1 ref_t= 300 300 300 300 Depending on the size of these groups, assigning them to separate thermostats may not be appropriate, and it doesn't appear that the protein is coupled anywhere. Consult http://www.gromacs.org/Documentation/Terminology/Thermostats Pcoupl = no gen_vel = yes gen_temp = 10 gen_seed = 173529 ; GolP has been tested with lincs only Then why turn off constraints? constraints = none constraint_algorithm = lincs lincs_order = 4 lincs_iter = 1 lincs_warnangle = 80 freezegrps = AU AUI freezedim= Y Y Y Y Y Y comm_mode = None Are these .mdp file right? No. See points above. I can't comment on whether any of the settings are correct for use with the GolP force field, but there are numerous inconsistencies from a generic standpoint. -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
Re: [gmx-users] Re: Simulation of 2D lattice model
On 1/17/13 1:31 PM, James Starlight wrote: Justin, so following to that equation the alteration of sigma will affect on both C6 and C12 ( attractive and repuslive terms). I dont quite understand how such modifications of the c6 and c12 params will change vdw radius of atom. I need some example to understand it :( You're not changing the van der Waals radius by doing that, you're changing the balance of interactions between the electron clouds of the particles in question. Refer to any basic textbook on what the Lennard-Jones equation is and what it means. Even the Wikipedia article provides a reasonable theoretical explanation. -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
Re: [gmx-users] Re: Simulation of 2D lattice model
Justin, so its exacly what I mean! I dont find any relationship between LJ equation in any form and vdw radius of atom. But is it possible to modify vdw radius exactly ? E.g I have united atom as a node which vdw must be 1.5 A. I want to decrease it to 1 A. What should I do for it ? James 2013/1/17 Justin Lemkul jalem...@vt.edu: You're not changing the van der Waals radius by doing that, you're changing the balance of interactions between the electron clouds of the particles in question. -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] Re: Simulation of 2D lattice model
On 1/17/13 2:05 PM, James Starlight wrote: Justin, so its exacly what I mean! I dont find any relationship between LJ equation in any form and vdw radius of atom. But is it possible to modify vdw radius exactly ? E.g I have united atom as a node which vdw must be 1.5 A. I want to decrease it to 1 A. What should I do for it ? There is no term in any potential energy equation (at least, in the force fields used by Gromacs) for an explicitly defined van der Waals radius. -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
Fw: [gmx-users] au--protein separate equilibration
Dear Justin thanks for your reply and, Please help me to correct the settings of .mdp files step by step . By these em.mdp files if I freeze only protein for the first time and after minimization I use the result .pdb file for second step of minimization that I freeze AU atoms in it, minimization would be true? title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein freezedim = Y Y Y comm_mode = None 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None -- 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] au--protein separate equilibration
On 1/17/13 2:48 PM, fatemeh ramezani wrote: Dear Justin thanks for your reply and, Please help me to correct the settings of .mdp files step by step . I did that in my previous reply. By these em.mdp files if I freeze only protein for the first time and after minimization I use the result .pdb file for second step of minimization that I freeze AU atoms in it, minimization would be true? I don't understand the purpose of freezing anything during EM; that sort of defeats the purpose of optimizing geometry. You can approach your problem however you see fit. -Justin title = n.pdb cpp= /lib/cpp define = -DFLEXIBLE constraints= none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist= 5 ns_type= grid rlist = 1 coulombtype= PME rcoulomb= 1 rvdw= 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein freezedim = Y Y Y comm_mode = None 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints= none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist= 5 ns_type= grid rlist = 1 coulombtype= PME rcoulomb = 1 rvdw= 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps =AU AUIAUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None -- 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] RE: gmx-users Digest, Vol 105, Issue 88
Dear Justin, For example, In hemoglobin (A-H helix), the particular E and F helix gets moved during the MD simulation, I would like to calculate this helix movements/rotation angle? Thanks. You'll have to define what you mean by helix movements. Everything moves in a simulation, but what is it that you're trying to quantify? If it's secondary structure itself, use do_dssp. If you're after something else, you will have to be more specific ---Original Message--- From: gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent date: 2013-01-17 22:02:54 GMT +0900 (ROK) Subject: gmx-users Digest, Vol 105, Issue 88 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Re: Simulation of 2D lattice model (Bogdan Costescu) 2. conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format (Anna Marabotti) 3. Re: conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format (Justin Lemkul) 4. Re: conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format (Daniel Larsson) 5. Movements of secondary structure (?) 6. Re: Re: Simulation of 2D lattice model (James Starlight) 7. Re: Movements of secondary structure (Justin Lemkul) -- Message: 1 Date: Thu, 17 Jan 2013 12:03:46 +0100 From: Bogdan Costescu bcoste...@gmail.com Subject: Re: [gmx-users] Re: Simulation of 2D lattice model To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cah+wpduv-uyezfoz7cjrzj_-5mjruur5j8qjtoshoodg9jm...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Thu, Jan 17, 2013 at 10:59 AM, James Starlight jmsstarli...@gmail.com wrote: thank you for so detailed explanation. You're welcome. Now it's up to you to use it :) Now it's only intresting to me if it possible to change vdw radius (assuming it as the distance from center of atom to it outer electronic shell)? Yes, it's possible. E.g I want to change such value for each node in my lattice model (e.g for CH2 united atom that value might be 1.5 and I want dicrease it to the 1 A ( as for simple carbon). Might I do it via some simplest modifications in the nonbonded.itp or should I do that by means of changes in sigma/epsillon terms (Which I also must express from A(c6) and B(c12) based on gromac's combination rules) ? If nonbonded.itp for your chosen force field is expressed in sigma/epsilon (I guess that this is the case because you talk about an existing value for sigma), then it's only a matter of changing the sigma parameter of that atomic species. Keep in mind that this is only a description of the change - it doesn't guarantee that the change is valid. If I'd be a reviewer I'd ask for a reason for changing one of the parameters (sigma) and keeping the other (epsilon) constant. Cheers, Bogdan -- Message: 2 Date: Thu, 17 Jan 2013 12:22:02 +0100 From: Anna Marabotti amarabo...@unisa.it Subject: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format To: gmx-users@gromacs.org Message-ID: 50f7deda.5090...@unisa.it Content-Type: text/plain; charset=ISO-8859-15; format=flowed Dear all, we'd need to convert a trajectory in .xtc format (and the related topology file) to a format that could be read by Amber program (I'd need to perform MM-PBSA calculations). We tried to do it using VMD, but failed to produce a correct trajectory to be read by MMPBSA.py tool. It complains about the fact that it expected only 3 or 6 box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9 box coords. I read the gmx-user archive to find hints to overcome the problem, but only found incomplete, and in some cases quite old, suggestions (We are currently using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on how to proceed, and I have even the doubt that this is not possible to do. Could you please give me some information about, possibly with detailed descriptions about the commands and the flags to use? Many thanks in advance for your kind answer and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via
Re: [gmx-users] Movements of secondary structure
Please use an appropriate subject line and delete irrelevant parts of the digest. On 1/17/13 8:42 PM, 라지브간디 wrote: Dear Justin, For example, In hemoglobin (A-H helix), the particular E and F helix gets moved during the MD simulation, I would like to calculate this helix movements/rotation angle? Thanks. RMSD (g_rms and/or g_rmsf -od), intramolecular distances (g_dist), helical rotation (g_helix) should all provide useful information. Please consult Chapter 8 of the manual to understand the quantities that Gromacs can calculate and the methods for doing so. -Justin You'll have to define what you mean by helix movements. Everything moves in a simulation, but what is it that you're trying to quantify? If it's secondary structure itself, use do_dssp. If you're after something else, you will have to be more specific -- 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] secondary structure movments
p{margin:0;padding:0;}
Dear Justin,
For example, In hemoglobin (A-H helix), the particular E and F helix gets moved
during the MD simulation, I would like to calculate this helix
movements/rotation angle? Thanks.
Dear all,
I have been trying to calculate and plot the secondary structure of helix
movements during the simulation on time through g_helix, g_helix orient,
g_principle and g_mindist but none of them shown the helix movements.
Is there any other tool can elaborate the helix movements ? Plz suggestion
are appreciated.
You'll have to define what you mean by helix movements. Everything moves in a
simulation, but what is it that you're trying to quantify? If it's secondary
structure itself, use do_dssp. If you're after something else, you will have to
be more specific.
-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
