Re: [gmx-users] pdb2gmx: how to preserve original ions?
On 7/17/18 9:22 PM, Anderson, Amos wrote: Hi Gromacs users, I’ve never used gromacs before, so sorry if this question has an obvious answer somewhere — it seems like the sort I should have been able to find an answer for… I want to write a python script to prepare an arbitrary pdb for use with gromacs (e.g., does these steps http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html for the user). The input pdb to my script may have waters, ions, and ligand(s) in it already. In the tutorial it says "you are going to want to strip out the crystal waters, PO4, and BME. Note that such a procedure is not universally appropriate (i.e., the case of a bound active site water molecule).” The wording maybe implies that other than active site waters and the ligand of interest, I’d never want to preserve HETATOMs in my input file? If not, and if I do want to keep them, how do I? Do I just treat all of them like ligands in the tutorial, e.g., maybe a protocol like this (more precise for ions I care about)? * grep HETATOM my.pdb > hetatoms.pdb HETATM, but yes. * gmx editconf -f hetatoms.pdb -o hetatoms.gro * copy/paste hetatoms.gro into my main .gro file (is there python/utility anywhere for merging .gro files I could leverage?) Conversion to .gro format is unnecessary; GROMACS handles PDB and other formats, if you prefer. * for ions gromacs doesn’t already know about (ions.itp), follow the instructions described here: http://www.mdtutorials.com/gmx/complex/02_topology.html Parametrization servers won't generally deal with monoatomic species. In a pairwise additive force field, the charge is already fixed and LJ have to be tuned, typically based on free energy of solvation. (in other words, I’m puzzled why pdb2gmx is complaining about ions it should already know about from the built-in ions.itp) pdb2gmx doesn't know anything about ions.itp, that comes in later when calling grompp. pdb2gmx only knows about what is defined in the force field .rtp file(s). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx: how to preserve original ions?
Hi Gromacs users, I’ve never used gromacs before, so sorry if this question has an obvious answer somewhere — it seems like the sort I should have been able to find an answer for… I want to write a python script to prepare an arbitrary pdb for use with gromacs (e.g., does these steps http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html for the user). The input pdb to my script may have waters, ions, and ligand(s) in it already. In the tutorial it says "you are going to want to strip out the crystal waters, PO4, and BME. Note that such a procedure is not universally appropriate (i.e., the case of a bound active site water molecule).” The wording maybe implies that other than active site waters and the ligand of interest, I’d never want to preserve HETATOMs in my input file? If not, and if I do want to keep them, how do I? Do I just treat all of them like ligands in the tutorial, e.g., maybe a protocol like this (more precise for ions I care about)? * grep HETATOM my.pdb > hetatoms.pdb * gmx editconf -f hetatoms.pdb -o hetatoms.gro * copy/paste hetatoms.gro into my main .gro file (is there python/utility anywhere for merging .gro files I could leverage?) * for ions gromacs doesn’t already know about (ions.itp), follow the instructions described here: http://www.mdtutorials.com/gmx/complex/02_topology.html (in other words, I’m puzzled why pdb2gmx is complaining about ions it should already know about from the built-in ions.itp) Thanks for any advice, Amos. To help future googlers, I run pdb2gmx on a file that has CL in it like this: gmx_d pdb2gmx -v -o output.gro -p output.top -ignh -water tip3p -ff charmm27 -f my.pdb I get this error: Program: gmx pdb2gmx, version 2016.3 Source file: src/gromacs/gmxpreprocess/resall.cpp (line 649) Fatal error: Residue 'CL' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors which surprises me because CL is defined in ions.itp. It says it’s finding other files in the same directory as ions.itp, so it doesn’t seem like some kind of misconfigured software install. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem in energy minimization
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision On Tue, 17 Jul. 2018, 11:12 pm neelam wafa, wrote: > Hi, > > Dear gromacs users, I am running md simmulation of a protein with a ligand. > i have already done it with the same protein and a different ligand. Now > when i run em md run i get following result. > > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 1000 (which may not be possible for your > system). > It stopped because the algorithm tried to make a new step whose size was > too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 150 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -9.3659806e+05 > Maximum force = 1.0269271e+04 on atom 4399 > Norm of force = 9.8929054e+01 > > NOTE: 10 % of the run time was spent in pair search, > you might want to increase nstlist (this has no effect on accuracy) > please guide me is it reliable to proceede for simmulation. or there is > something wrong. Is it a sign of system instability? > > looking forward for your cooperation. > > Regards > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Reaching equilibrium
Monitor your property of interest, then when it has reached a stable value for a length of time (need to consider how long takes to stabilise to how long that should be), then you can start to think it may be at "equilibrium". Depending on the property of interest though, you have to chance if ran bit longer it may flip into another, more stable state. But you need to draw the line somewhere. On Wed, 18 Jul. 2018, 12:22 am SHYANTANI MAITI, wrote: > Dear all, > How to understand whether a system(large system) reaches equilibrium after > MD simulation? > > -- > Best regards, > *Shyantani Maiti* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: problem in energy minimization
-- Forwarded message -- From: neelam wafa Date: Tue, Jul 17, 2018 at 1:12 PM Subject: problem in energy minimization To: gromacs.org_gmx-users@maillist.sys.kth.se Hi, Dear gromacs users, I am running md simmulation of a protein with a ligand. i have already done it with the same protein and a different ligand. Now when i run em md run i get following result. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 150 steps, but did not reach the requested Fmax < 1000. Potential Energy = -9.3659806e+05 Maximum force = 1.0269271e+04 on atom 4399 Norm of force = 9.8929054e+01 NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) please guide me is it reliable to proceede for simmulation. or there is something wrong. Is it a sign of system instability? looking forward for your cooperation. Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Incorrect number of parameters in improper dihedral
Hello, In the OPLSAA ffbonded.itp, it is also mentioned that improper torsions for planar groups are implemented in gromacs as proper dihedrals. So, I think you are using the wrong function type here (type 2); you should use type 1 in this case. Hope this helps. Best, Abhishek On Tue, Jul 17, 2018 at 6:05 AM, Debadutta Prusty < debaduttaprusty1.2...@u.northwestern.edu> wrote: > Hi everyone, > > I ran an energy minimization run on a single polymer chain. On running the > gmx grompp -f .mdp , I get the following error message: > "ERROR 1 [file topol.top, line 1486]: > Incorrect number of parameters - found 3, expected 2 or 4 for Improper > Dih." > > The corresponding line(line 1486) in the topology file is: > ; aiajakal functc0c1 > c2c3 > 8 7 115 2improper_X_CA_Y_Z > > The entry containing the definition of this forcefield in the ffbonded.itp > (I am using opls all atom force field) file is > ; X-CA-Y-Z improper torsion. CA is any ring carbon in pyridine > #define improper_X_CA_Y_Z 180.0 10.460 2 > > The topology file for the above polymer was generated by using the command > pdb2gmx(it operated on the pdb file of the polymer chain). > > Please help me out. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] resize pre-equilibrated system
Hi Justin, Thank you for getting back to me. After estimating the resulting reduction in system size, in this case I decided to live with the extra water molecules. However, it’s good to know that any system adjusted this way requires both minimization and equilibration. Best, Roman > On Jul 13, 2018, at 4:52 PM, Justin Lemkul wrote: > > > > On 7/13/18 12:07 PM, Roman Sloutsky wrote: >> I have been simulating a system of protein in explicit water under PBC. When >> I first prepared the system for simulation, the protein had an extended >> flexible linker (it was modeled in). I surrounded it with a water box with >> some padding past the edge of the extended linker. >> >> During the simulation I’ve already performed the linker collapsed into a >> globular conformation, and now I have an excess amount of water surrounding >> the protein. I expect this collapsed configuration to persist for a long >> time, so I would like to avoid simulating all that bulk water unnecessarily. >> On the other hand, the system is already equilibrated, and I would rather >> not re-solvate the new configuration of the protein from scratch. >> >> Is it possible to use gmx tools to re-size the system and remove the excess >> water molecules, maintaining the position of the protein at the center of >> the unit box? Maintaining the velocities of the remaining molecules (to >> avoid any additional equilibration) would be a nice bonus, but equilibrating >> from the last frame of a well-behaved simulation would still be better than >> equilibrating a new system. >> >> I do have counter ions, some of which might end up betting excluded and >> would need to be placed back into the new box. Therefore, some minimal >> equilibration might still be required. > > You're definitely going to need re-equilibration. You can probably carve out > the system you want with gmx select to create a geometry-based index group, > then gmx trjconv to save only those atoms from an existing frame, but there's > no point trying to preserve velocities or anything. You're now creating a new > periodic system with interactions that were not previously present, and may > have clashes or non-optimal geometries. You can save your coordinates as you > like, but you should minimize and equilibrate as if it were a new system; > there's no way to do a "continuous" simulation in this case. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Reaching equilibrium
Dear all, How to understand whether a system(large system) reaches equilibrium after MD simulation? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Lennard-Jones mixture with non-standard mixing rules and different interaction cut-offs -- simple way to implement?
Hello all, I'd like to simulate a Lennard-Jones mixture. For simplicity, let's say it's a binary A B mixture. However, sigma_AB and epsilon_AB are set independently (i.e. NOT derived from a standard mixing rule of AA and BB parameters). In addition, I'd like AA, BB, and AB interactions to all have different interaction cut-offs. Is this possible to implement in a simple manner or does this require using a tabulated potential? Thanks! -Elia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem in energy minimization
Hi, Dear gromacs users, I am running md simmulation of a protein with a ligand. i have already done it with the same protein and a different ligand. Now when i run em md run i get following result. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 150 steps, but did not reach the requested Fmax < 1000. Potential Energy = -9.3659806e+05 Maximum force = 1.0269271e+04 on atom 4399 Norm of force = 9.8929054e+01 NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) please guide me is it reliable to proceede for simmulation. or there is something wrong. Is it a sign of system instability? looking forward for your cooperation. Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] what is the force on the energy group when pullcode is used?
one more question about the pull code. I have outputted the force for pulling the molecule in .xvg file. If I pulled the molecule in Z direction, does the positive sign in front of the force mean the direction of the pulling force is identical to the positive direction of the Z axis? Fan -- Original -- From: "Justin Lemkul";; Date: Jul 17, 2018 To: "gmx-users"; Subject: Re: [gmx-users] what is the force on the energy group when pullcode is used? On 7/17/18 6:03 AM, 1185201182 wrote: > Dear users > > > I am using the pull code to pull one of molecules in my simulation and the > molecule which is pulled is also defined as an energy group in my mdp file, > then I output the force in trr file > > > > So I wonder if the force on the pulled molecule in the trr file just includes > the force from potentials , or it also includes the force from the pull code. The forces written to the .trr are not decomposed in any way, so it's the total force acting on the atom(s) selected. Energy groups have no relevance here. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Format of xvg file
Hi, Generally there is useful information in the header of the .xvg file, which people might be able to help interpret. They will also want to know what command you ran, and from what version of GROMACS, because these things can vary over time. Mark On Tue, Jul 17, 2018 at 2:37 PM SHYANTANI MAITI wrote: > Dear all, > What should be the format of xvg file for calculating the time correlation > function in gromacs? > I am using this format(1st and 3rd column are the time steps) > 0 -1.73312 0 5.43112 > 2 -0.84264 2 8.65560 > 4 -0.89785 4 2.14901 > 6 1.613256 2.87340 > 8 -2.32500 8 0.48249 > 10 1.82224 10 -1.97349 > 12 -4.46258 12 -7.37206 > 14 -1.92328 14 -3.90647 > 16 1.59936 16 -2.36261 > 18 4.20724 18 -4.91194 > 20 2.94238 20 0.93495 > > The output is coming as > 0.000 1.0 > 2.000 0.14903 > 4.000 0.02809 > 6.000-0.53731 > 8.000-0.13294 > 10.000 0.01311 > & > 0.000 1.0 > 2.000 0.8 > 4.000 0.56667 > 6.000 0.3 > 8.000 0.0 > 10.000-0.3 > & > 0.000 1.0 > 2.000 0.65426 > 4.000 0.38859 > 6.000 0.18424 > 8.000-0.28270 > 10.000-0.77704 > & > The other frames are missing..can you please suggest the exact file format > of xvg file to compute time correlation function? > > -- > Best regards, > *Shyantani Maiti* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] what is the force on the energy group when pullcode is used?
Thanks Justin Fan -- Original -- From: "Justin Lemkul";; Date: Jul 17, 2018 To: "gmx-users"; Subject: Re: [gmx-users] what is the force on the energy group when pullcode is used? On 7/17/18 6:03 AM, 1185201182 wrote: > Dear users > > > I am using the pull code to pull one of molecules in my simulation and the > molecule which is pulled is also defined as an energy group in my mdp file, > then I output the force in trr file > > > > So I wonder if the force on the pulled molecule in the trr file just includes > the force from potentials , or it also includes the force from the pull code. The forces written to the .trr are not decomposed in any way, so it's the total force acting on the atom(s) selected. Energy groups have no relevance here. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Format of xvg file
Dear all, What should be the format of xvg file for calculating the time correlation function in gromacs? I am using this format(1st and 3rd column are the time steps) 0 -1.73312 0 5.43112 2 -0.84264 2 8.65560 4 -0.89785 4 2.14901 6 1.613256 2.87340 8 -2.32500 8 0.48249 10 1.82224 10 -1.97349 12 -4.46258 12 -7.37206 14 -1.92328 14 -3.90647 16 1.59936 16 -2.36261 18 4.20724 18 -4.91194 20 2.94238 20 0.93495 The output is coming as 0.000 1.0 2.000 0.14903 4.000 0.02809 6.000-0.53731 8.000-0.13294 10.000 0.01311 & 0.000 1.0 2.000 0.8 4.000 0.56667 6.000 0.3 8.000 0.0 10.000-0.3 & 0.000 1.0 2.000 0.65426 4.000 0.38859 6.000 0.18424 8.000-0.28270 10.000-0.77704 & The other frames are missing..can you please suggest the exact file format of xvg file to compute time correlation function? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] what is the force on the energy group when pull code is used?
On 7/17/18 6:03 AM, 1185201182 wrote: Dear users I am using the pull code to pull one of molecules in my simulation and the molecule which is pulled is also defined as an energy group in my mdp file, then I output the force in trr file So I wonder if the force on the pulled molecule in the trr file just includes the force from potentials , or it also includes the force from the pull code. The forces written to the .trr are not decomposed in any way, so it's the total force acting on the atom(s) selected. Energy groups have no relevance here. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Grompp errors while changing combination rules
On 7/17/18 5:40 AM, Apramita Chand wrote: Dear All, I had enquired earlier about the steps for changing combination rules in GROMOS ff. As I understood from your answers, if I am to take combination rule 3, I can put sigma and epsilon for my atomtypes under the C6 and C12 columns in ffnonbonded.itp and these numbers will be interpreted as sigma and epsilon when I specify the combination number. Also, I don't need to add anything in the non-bonded params section as the interactions will be automatically calculated. I have specified the 'gen-pairs'=yes in the The gen-pairs keyword has no real relation to the combination rule, it's there to do what it says: generate 1-4 pair parameters when not present in ffnonbonded.itp. defaults section for this purpose. But when I try to minimise the system I get the message: Too many warnings (2862), g_grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. WARNING 2862 [file ffnonbonded_modified.itp, line 2927]: Too few parameters on line (source file /builddir/build/BUILD/gromacs-4.5.7/src/kernel/toppush.c, line 820) Any reason you are using wildly outdated (and unsupported) software? I had taken the exact same system and files with combination rule 1 and the simulation ran smoothly. What could be the problem? Is there anything I have missed out ?Should I use the maxwarn option? Absolutely not. "Too few parameters on line" means the format of what you have provided grompp is not correct. Your model physics will not be realistic, if the resulting simulation even runs. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Tilt in the Bilayer
On 7/17/18 3:10 AM, atb files wrote: Dear experts,How can I find the tilt in the lipids of the Bilayer with respect to Bilayer normalAny gromacs tool which can do this.ThanksYogiSent using Zoho Mail gmx bundle and gmx gangle can both do this. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problems during installation
Justin,
Lovely advice. I'll definitely consider it :) Thank you.
Regards,
Rajat
On Mon, Jul 16, 2018 at 11:15 PM Justin Lemkul wrote:
>
>
> On 7/16/18 1:42 PM, Rajat Desikan wrote:
> > Hi Mark,
> >
> > Thank you for the quick answer. My group is experimenting with a
> GPU-heavy
> > processor-light configuration similar to the Amber machines available
> from
> > Exxact (https://www.exxactcorp.com/AMBER-Certified-MD-Systems). In our
> > understanding, for this configuration to be successful performance-wise,
> > gromacs would've to do all the calculating on GPUs, and not just
> > electrostatics. That's why we're looking at openmm enabled versions.
> >
> > If you and others have alternate suggestions, we would be really eager to
> > hear them. Thank you for your time.
>
> IIRC, the OpenMM code in GROMACS only ever did implicit solvent
> calculations. With GROMACS 2018, all the nonbonded calculations are done
> on GPU with PME offload, which sounds exactly like what you want. You
> should be using a current version, not an ancient one :)
>
> -Justin
>
> > Regards,
> > Rajat
> >
> > On Mon, 16 Jul 2018, 10:25 pm Mark Abraham,
> > wrote:
> >
> >> Hi,
> >>
> >> This code was not ever functional in the 4.6 branch, so if you want it
> to
> >> work, try 4.5.7. But really there is no reason to want to build it any
> more
> >> - use the CUDA and OpenCL ports available in more recent GROMACS.
> >>
> >> Mark
> >>
> >> On Mon, Jul 16, 2018 at 6:47 PM Rajat Desikan
> >> wrote:
> >>
> >>> Dear all,
> >>> I'm trying to install openmm enabled version of gromacs 4.6.7 on a
> 6-core
> >>> i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
> >>> strange error while running make:
> >>>
> >>> /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function
> >> ‘cmain’:
> >>> /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
> >>> missing braces around initializer [-Wmissing-braces]
> >>> gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
> >>> ^
> >>> */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note:
> (near
> >>> initialization for ‘hw_opt’)*
> >>> */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
> >>> ‘gmx_hw_opt_t {aka struct }’ has no member named ‘gpu_id’;
> did
> >>> you mean ‘gpu_opt’?*
> >>> * { "-gpu_id", FALSE, etSTR, {_opt.gpu_id},*
> >>> ^
> >>> src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
> >>> 'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
> >>> make[2]: ***
> >> [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]
> >>> Error 1
> >>> CMakeFiles/Makefile2:1902: recipe for target
> >>> 'src/kernel/CMakeFiles/mdrun.dir/all' failed
> >>> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
> >>> Makefile:162: recipe for target 'all' failed
> >>> make: *** [all] Error 2
> >>>
> >>> I have installed cuda 9.1, openmm, fftw, open-mpi and all other
> necessary
> >>> software, so I'm at a loss. Please help me out. Google did not have
> much
> >>> leads.
> >>>
> >>> Thank you.
> >>>
> >>> Regards,
> >>> Rajat
> >>>
> >>> --
> >>> Dr. Rajat Desikan (Post Doctoral Fellow)
> >>> Prof. Narendra M Dixit's Lab (no 1),
> >>> Dept. of Chemical Engineering,
> >>> Indian Institute of Science, Bangalore
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>> posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-requ...@gromacs.org.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
--
Dr. Rajat Desikan (Post Doctoral Fellow)
Prof. Narendra M Dixit's Lab (no 1),
Dept. of
[gmx-users] what is the force on the energy group when pull code is used?
Dear users I am using the pull code to pull one of molecules in my simulation and the molecule which is pulled is also defined as an energy group in my mdp file, then I output the force in trr file So I wonder if the force on the pulled molecule in the trr file just includes the force from potentials , or it also includes the force from the pull code. Thanks for your help. Fan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Grompp errors while changing combination rules
Dear All, I had enquired earlier about the steps for changing combination rules in GROMOS ff. As I understood from your answers, if I am to take combination rule 3, I can put sigma and epsilon for my atomtypes under the C6 and C12 columns in ffnonbonded.itp and these numbers will be interpreted as sigma and epsilon when I specify the combination number. Also, I don't need to add anything in the non-bonded params section as the interactions will be automatically calculated. I have specified the 'gen-pairs'=yes in the defaults section for this purpose. But when I try to minimise the system I get the message: Too many warnings (2862), g_grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. WARNING 2862 [file ffnonbonded_modified.itp, line 2927]: Too few parameters on line (source file /builddir/build/BUILD/gromacs-4.5.7/src/kernel/toppush.c, line 820) I had taken the exact same system and files with combination rule 1 and the simulation ran smoothly. What could be the problem? Is there anything I have missed out ?Should I use the maxwarn option? Your help will be highly appreciated. Thanking you, Yours sincerely, Apramita Chand -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Tilt in the Bilayer
Dear experts,How can I find the tilt in the lipids of the Bilayer with respect to Bilayer normalAny gromacs tool which can do this.ThanksYogiSent using Zoho Mail -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pressure Calculation in Gromacs
Hi, That depends what your other inputs are. See the reference manual, chapter 2. Mark On Tue, Jul 17, 2018 at 5:05 AM Brandon Wiebe wrote: > Thank you, Justin. > > So if I wanted to simulate a system of Lennard-Jones particles under the > NPT ensemble using reduced units, would I need to set ref_p to P*, or > PRESFAC*(P*)? > > Regards, > Brandon > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin > Lemkul [jalem...@vt.edu] > Sent: Monday, July 16, 2018 7:23 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Pressure Calculation in Gromacs > > On 7/16/18 9:55 PM, Brandon Wiebe wrote: > > Hi there, > > > > I am wondering if anyone can break down exactly how the instantaneous > pressure of any given frame is calculated in Gromacs? > > > > According to section 3.4.3 of the manual, the pressure tensor is given > by: P = (2/V) * (Ek - W), where Ek is kinetic energy and W is the virial. > > I have taken a particular frame and calculated the volume, kinetic > energy and virial. > > My calculated quantities all match quite closely with the values > reported by Gromacs, however, the pressure that I get is significantly > lower than the value reported by Gromacs. > > The elements of my calculated pressure tensor are all approximately 16.5 > times smaller than those reported by Gromacs, even though the component > quantities that go into the pressure calculation are nearly identical. > > There's a unit conversion factor (see src/gromacs/math/units.h): > > /* Pressure in MD units is: > * 1 bar = 1e5 Pa = 1e5 kg m^-1 s^-2 = 1e-28 kg nm^-1 ps^-2 = 1e-28 / > AMU amu nm^1 ps ^2 > */ > #define BAR_MDUNITS (1e5*NANO*PICO*PICO/AMU) > #define PRESFAC (1.0/BAR_MDUNITS) > > PRESFAC works out to be 16.6. > > -Justin > > > I have repeated this calculation for a number of frames, and have tried > using Gromacs 4.6.7 and 5.0.4 to no avail. > > Clearly there is some systematic error in my methodology, where could > this discrepancy come from? > > > > Regards, > > Brandon > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
