Re: [gmx-users] Running MD only for selected part of molecule
Hi Justin, Thanks for your reply... and apologies for asking you again. If I want to keep a part of my molecule fix, say part out of 12 angstrom radius from the ligand and also want to make avoid energy calculation for the same, (using energy_excl) Do I need to mention the separate group for that part of molecule, (as I already did to make that part position restrained), and next how I will mention those part in .mdp file... Is it like... energy_excl groupname protein/solvent (if I want to avoid energy calculation between the group and protein/solvent) or something else need to be done than that (like during genpr option). Please explainAs I have no idea to play with such option... My apologies again, if these small question irritates you... With Thanks, Vivek 2008/10/15 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Dear Justin, Thanks for your reply.. But I am not getting how and where should I give the option of energy_excl. For freezing a part of molecule ? In the .mdp file. what are the other checks to be done for the same ? I don't know what you're asking. -Justin With Thanks, Vivek 2008/10/14 Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] vivek sharma wrote: 2008/10/14 Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] vivek sharma wrote: Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for the same), thanks for your suggestions regarding the same. But, I have seen that the part of the molecule I kept for PR is still having some motion, how can I keep that part rigid ? Position restraints do not necessarily guarantee that atomic positions stay absolutely fixed. Instead, there is an energy penalty for moving them, which could in some cases be overcome. I am not getting any idea of energy_excl option mentioned above, please explain. The freezegrps option can be used to fix atomic positions, but in this case large forces can be generated within the frozen group. As such, you can apply energygrp_excl to exclude energetic terms within the frozen group. Will it help me in reducing the time taken for the simulation if I'll keep the part of molecule frozen ? I've never used freezegrps for any large set of atoms, so maybe. If you've got surrounding solvent, though, the nonbonded interactions are still calculated between the frozen group and solvent, unless you turn that off too. But then it starts getting really unphysical, in my view. -Justin Thanks, ~Vivek -Justin With Thanks, Vivek 2008/10/12 Erik Lindahl [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Hi, On Oct 10, 2008, at 12:46 PM, Justin A. Lemkul wrote: I want to run MD over a part of my molecule , for few residues only (not the whole molecule). Can I do it using GROMACS ? I searched for the online documentation and mailing list, but unable to get appropriate information. If somebody has already tried such things earlier, please suggest and direct me for appropriate link and address. Well, if your goal is to keep certain parts fixed and allow others to move, probably the easiest way to do it is to apply position restraints to the fixed part. You can also set parts of the system as a freeze group, in which case you can exclude all nonbonded interactions inside the freeze group with the energygrp_excl option in your mdp file. The main advantage of this is of course that you will improve performance if 99% of your system is frozen (although all interactions between the frozen and non-frozen parts still have to be calculated). On the other hand, completely freezing part of the system is not very realistic, and you're likely to get strange behavior in the
[gmx-users] ErrorBox was shifted at least 10 times. Please see log-file
Hi Tehre, i am running a job by keeping a part of molecule freeze by using the .mdp option __ energygrps_excl= Terminal Terminal Terminal SOL ! To remove computation of nonbonding interactions between the frozen groups with each other and surroundings (i.e. the solvent, SOL) freezegrps = Terminal ! Index group to freeze freezedim = Y Y Y ! Freeze this group in all directions, x, y, and z ___ where frreze is a group mentioned in the index file... During the run the job is being terminated with the following error . __ Step 1 Warning: pressure scaling more than 1%, mu: -3.51079e+22 -3.51079e+22 -3.51079e+22 --- Program mdrun_d, VERSION 3.3.3 Source code file: ns.c, line: 258 Fatal error: Box was shifted at least 10 times. Please see log-file. --- Error on node 0, will try to stop all the nodes Halting parallel program mdrun_d on CPU 0 out of 24 srun: error: n216: task0: Aborted srun: Terminating job __ Can somebody give an insight in the problem for figuring out the probable cause of the error. PS::Before the run I mentioned the boxsize in editconf as -box 7.5 5 6 , to keep the size of box and number of solvent optimum. Does it have anything to do with the mentioned error ? Looking for suggestions.. with thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] range of gen_seed
Hi everyone, I want to start from the same starting structure with different velocities. In the .mdp file. I used 3 different values for gen_seed for three different runs : 1. one is the default, the other two are 1 and 571. I want to know that does this ensure that the mdrun starts with diffrent velocities ? Is there any defined range for the random number generator? Thanks in advance.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trjconv in Parallel run
Hi all, I have been running mdrun in Parallel for few hours due to full disk it crashed in between, later when I use trjconv command trjconv -f .trr -o xtc for convert .trr to .xtc its showing Program trjconv, VERSION 3.3.1 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file cant I make .trr to .xtc? what may be the problem how can I remedy this error. Any suggestions would be appreciated Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] range of gen_seed
I believe that (-1) as the seed takes the time or something as the actual seed, thus ensuring no two identical seeds, and no two identical velocities. Omer. On Fri, Oct 17, 2008 at 12:11, sarbani chattopadhyay [EMAIL PROTECTED] wrote: I want to know that does this ensure that the mdrun starts with diffrent velocities ? Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem building a new polymer using pdb2gmx....
Dear David (van der Spoel) I made a trial with pdb2gmx using -ter option as you suggested but without success. I also tried with -inter option but it didn't work. The program did not give me any chance to reject the option of adding TER or other kind of atoms. It just gives me the same error. Am I doing something wrong? I have also read a lot of messages in the gromacs list related with pdb2gmx errors but no one give me any idea of how to resolve my problem. The reading of chapter 5 of gromacs manual neither. I found in the gromacs list many people complaining about pdb2gmx looked for atoms which it didn't exist in their pdb's or rtp files. Quite similar to my problem, but aparently they were able to solve it. Below I am adding the complete error mesagge of pdb2gmx, may be you can give any clue of what is happening. Opening library file ffG53a6.rtp Opening library file aminoacids.dat Reading polymer.gro... Read 'Generated by trjconv : 14 TEQ-VBT 1:1 t= 1750.00024', 309 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 14 residues with 309 atoms chain #res #atoms 1 '-'14309 No occupancies in polymer.gro Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.atp Atomtype 57 Reading residue database... (ffG53a6) Opening library file ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 119 Sorting it all out... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.hdb Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6-n.tdb Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6-c.tdb Processing chain 1 (309 atoms, 14 residues) --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom H1 in residue VBT 2 not found in rtp entry with 24 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. I'm trying to build a polymer with a new building block. I have included the new topology block inside the force field rtp file, which I've choosen for my simulation (ffG53a6.rtp). I've also prepared a gro input file, where the atoms of each residue follows the same order as in the rtp file I also added the new residues names in aminoacids.dat The problem is: when I run pdb2gmx to obtain the topology of my system it gives me the following error: Fatal error: Atom H1 in residue VBT 2 not found in rtp entry with 24 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. But there's no H1 atom in my residues. Is pdb2gmx including some extra atoms to complete my molecule? Could anyone give any clue about my problem? David van der Spoel wrote: yes. pdb2gmx thinks your molecule is a protein and want to add Hydrogens to the termini. Use the -ter flag and select None. below there's a part of my rtp file ... [ VBT ] [ atoms ] ; name type charge chargegroup CC1 CH2 0.0 1 CC2 CH1 0.12000 2 CR1 C-0.12000 3 CR2 C-0.14000 4 HR2HC 0.14000 4 CR3 C-0.08000 5 HR3HC 0.08000 5 CR4 C-0.05000 6 CT1 CH2 0.37000 6 NT1NR-0.32000 6 CR5 C-0.13000 7 HR5HC 0.13000 7 CR6 C-0.17000 8 HR6HC 0.17000 8 CT2 C-0.21000 9 HT1HC 0.21000 9 CT3 C-0.0900010 CT4 CH3 0.0900010 CT5 C 0.5800011 OT1 O-0.5800011 NT2NR-0.2200012 HT2 H 0.2200012 CT6 C 0.5400013 OT2 O-0.5400013 part of my *.gro file 2VBTCC1 21 3.221 5.305 1.589 2VBTCC2 22 3.143 5.334 1.460 2VBTCR1 23 3.115 5.221 1.384 2VBTCR2 24 3.196 5.155 1.293 2VBTHR2 25 3.305 5.159 1.298 2VBTCR3 26 3.132 5.074 1.200 2VBTHR3 27 3.198 5.003 1.151 2VBTCR4 28 2.995 5.068 1.175 2VBTCT1 29 2.948 5.023 1.052 2VBTNT1 30 3.028 5.038 0.928 2VBTCR5 31 2.919 5.144 1.263 2VBTHR5 32 2.810 5.142 1.268 2VBTCR6 33 2.977 5.208 1.372 2VBTHR6 34 2.916 5.232 1.459 2VBTCT2 35 3.070 4.916 0.874 2VBTHT1 36 3.009 4.827 0.860 2VBTCT3 37 3.190 4.911 0.804
Re: [gmx-users] trjconv in Parallel run
sudheer babu wrote: Hi all, I have been running mdrun in Parallel for few hours due to full disk it crashed in between, later when I use trjconv command trjconv -f .trr -o xtc for convert .trr to .xtc its showing Program trjconv, VERSION 3.3.1 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file have you tried trjconv -ndec ? Jochen cant I make .trr to .xtc? what may be the problem how can I remedy this error. Any suggestions would be appreciated Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] range of gen_seed
sarbani chattopadhyay wrote: Hi everyone, I want to start from the same starting structure with different velocities. In the .mdp file. I used 3 different values for gen_seed for three different runs : 1. one is the default, the other two are 1 and 571. I want to know that does this ensure that the mdrun starts with diffrent velocities ? You can have a look at the starting velocities by converting the tpr in a gro file with editconf. Jochen Is there any defined range for the random number generator? Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv in Parallel run
sudheer babu wrote: Hi all, I have been running mdrun in Parallel for few hours due to full disk it crashed in between, later when I use trjconv command trjconv -f .trr -o xtc for convert .trr to .xtc its showing Program trjconv, VERSION 3.3.1 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file That usually means something is corrupted; what does gmxcheck tell you about the .trr? -Justin cant I make .trr to .xtc? what may be the problem how can I remedy this error. Any suggestions would be appreciated Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ErrorBox was shifted at least 10 times. Please see log-file
vivek sharma wrote: Hi Tehre, i am running a job by keeping a part of molecule freeze by using the .mdp option What is your entire .mdp file? -Justin __ energygrps_excl= Terminal Terminal Terminal SOL ! To remove computation of nonbonding interactions between the frozen groups with each other and surroundings (i.e. the solvent, SOL) freezegrps = Terminal ! Index group to freeze freezedim = Y Y Y ! Freeze this group in all directions, x, y, and z ___ where frreze is a group mentioned in the index file... During the run the job is being terminated with the following error . __ Step 1 Warning: pressure scaling more than 1%, mu: -3.51079e+22 -3.51079e+22 -3.51079e+22 --- Program mdrun_d, VERSION 3.3.3 Source code file: ns.c, line: 258 Fatal error: Box was shifted at least 10 times. Please see log-file. --- Error on node 0, will try to stop all the nodes Halting parallel program mdrun_d on CPU 0 out of 24 srun: error: n216: task0: Aborted srun: Terminating job __ Can somebody give an insight in the problem for figuring out the probable cause of the error. PS::Before the run I mentioned the boxsize in editconf as -box 7.5 5 6 , to keep the size of box and number of solvent optimum. Does it have anything to do with the mentioned error ? Looking for suggestions.. with thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ErrorBox was shifted at least 10 times. Please see log-file
Hi justin, thanks for your response. following is the .mdp file pasted.. _ title = trp_drg warnings= 10 cpp = /lib/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 250 ; total 5000.0 ps. nstcomm = 1 nstxout = 25000 ; output coordinates every 0.5 ps nstvout = 10 ; output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 energygrps_excl = freeze freeze freeze SOL ! To remove computation of interactions between the frozen groups with surroundings (i.e. the solvent, SOL) fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.10.1 0.1 tc_grps = proteinsol NDP ref_t = 300300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ; Non-equilibrium MD stuff freezegrps = freeze freezedim= Y Y Y With Thanks, Vivek 2008/10/17 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Hi Tehre, i am running a job by keeping a part of molecule freeze by using the .mdp option What is your entire .mdp file? -Justin __ energygrps_excl= Terminal Terminal Terminal SOL ! To remove computation of nonbonding interactions between the frozen groups with each other and surroundings (i.e. the solvent, SOL) freezegrps = Terminal ! Index group to freeze freezedim = Y Y Y ! Freeze this group in all directions, x, y, and z ___ where frreze is a group mentioned in the index file... During the run the job is being terminated with the following error . __ Step 1 Warning: pressure scaling more than 1%, mu: -3.51079e+22 -3.51079e+22 -3.51079e+22 --- Program mdrun_d, VERSION 3.3.3 Source code file: ns.c, line: 258 Fatal error: Box was shifted at least 10 times. Please see log-file. --- Error on node 0, will try to stop all the nodes Halting parallel program mdrun_d on CPU 0 out of 24 srun: error: n216: task0: Aborted srun: Terminating job __ Can somebody give an insight in the problem for figuring out the probable cause of the error. PS::Before the run I mentioned the boxsize in editconf as -box 7.5 5 6 , to keep the size of box and number of solvent optimum. Does it have anything to do with the mentioned error ? Looking for suggestions.. with thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read
Re: [gmx-users] ErrorBox was shifted at least 10 times. Please see log-file
There are several potential problems all combined into one. As has been reported on the list, applying freezegrps, constraints, and pressure coupling all at the same time do not mix well. The best bet is to turn off the pressure coupling if you're set on using freezegrps. Otherwise, use position restraints if you require NPT. -Justin vivek sharma wrote: Hi justin, thanks for your response. following is the .mdp file pasted.. _ title = trp_drg warnings= 10 cpp = /lib/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 250 ; total 5000.0 ps. nstcomm = 1 nstxout = 25000 ; output coordinates every 0.5 ps nstvout = 10 ; output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 energygrps_excl = freeze freeze freeze SOL ! To remove computation of interactions between the frozen groups with surroundings (i.e. the solvent, SOL) fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.10.1 0.1 tc_grps = proteinsol NDP ref_t = 300300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ; Non-equilibrium MD stuff freezegrps = freeze freezedim= Y Y Y With Thanks, Vivek 2008/10/17 Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] vivek sharma wrote: Hi Tehre, i am running a job by keeping a part of molecule freeze by using the .mdp option What is your entire .mdp file? -Justin __ energygrps_excl= Terminal Terminal Terminal SOL ! To remove computation of nonbonding interactions between the frozen groups with each other and surroundings (i.e. the solvent, SOL) freezegrps = Terminal ! Index group to freeze freezedim = Y Y Y ! Freeze this group in all directions, x, y, and z ___ where frreze is a group mentioned in the index file... During the run the job is being terminated with the following error . __ Step 1 Warning: pressure scaling more than 1%, mu: -3.51079e+22 -3.51079e+22 -3.51079e+22 --- Program mdrun_d, VERSION 3.3.3 Source code file: ns.c, line: 258 Fatal error: Box was shifted at least 10 times. Please see log-file. --- Error on node 0, will try to stop all the nodes Halting parallel program mdrun_d on CPU 0 out of 24 srun: error: n216: task0: Aborted srun: Terminating job __ Can somebody give an insight in the problem for figuring out the probable cause of the error. PS::Before the run I mentioned the boxsize in editconf as -box 7.5 5 6 , to keep the size of box and number of solvent optimum. Does it have anything to do with the mentioned error ? Looking for suggestions.. with thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
Re: [gmx-users] Problem building a new polymer using pdb2gmx....
Alberto Sergio Garay wrote: Dear David (van der Spoel) I made a trial with pdb2gmx using -ter option as you suggested but without success. I also tried with -inter option but it didn't work. The program did not give me any chance to reject the option of adding TER or other kind of atoms. It just gives me the same error. Am I doing something wrong? I have also read a lot of messages in the gromacs list related with pdb2gmx errors but no one give me any idea of how to resolve my problem. The reading of chapter 5 of gromacs manual neither. I found in the gromacs list many people complaining about pdb2gmx looked for atoms which it didn't exist in their pdb's or rtp files. Quite similar to my problem, but aparently they were able to solve it. Below I am adding the complete error mesagge of pdb2gmx, may be you can give any clue of what is happening. please give the whole command line pdb2gmx -ignh -ter should be OK, but if you nee dhydrogens you also have to make/update the hdb file. Opening library file ffG53a6.rtp Opening library file aminoacids.dat Reading polymer.gro... Read 'Generated by trjconv : 14 TEQ-VBT 1:1 t= 1750.00024', 309 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 14 residues with 309 atoms chain #res #atoms 1 '-'14309 No occupancies in polymer.gro Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.atp Atomtype 57 Reading residue database... (ffG53a6) Opening library file ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 119 Sorting it all out... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.hdb Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6-n.tdb Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6-c.tdb Processing chain 1 (309 atoms, 14 residues) --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom H1 in residue VBT 2 not found in rtp entry with 24 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. I'm trying to build a polymer with a new building block. I have included the new topology block inside the force field rtp file, which I've choosen for my simulation (ffG53a6.rtp). I've also prepared a gro input file, where the atoms of each residue follows the same order as in the rtp file I also added the new residues names in aminoacids.dat The problem is: when I run pdb2gmx to obtain the topology of my system it gives me the following error: Fatal error: Atom H1 in residue VBT 2 not found in rtp entry with 24 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. But there's no H1 atom in my residues. Is pdb2gmx including some extra atoms to complete my molecule? Could anyone give any clue about my problem? David van der Spoel wrote: yes. pdb2gmx thinks your molecule is a protein and want to add Hydrogens to the termini. Use the -ter flag and select None. below there's a part of my rtp file ... [ VBT ] [ atoms ] ; name type charge chargegroup CC1 CH2 0.0 1 CC2 CH1 0.12000 2 CR1 C-0.12000 3 CR2 C-0.14000 4 HR2HC 0.14000 4 CR3 C-0.08000 5 HR3HC 0.08000 5 CR4 C-0.05000 6 CT1 CH2 0.37000 6 NT1NR-0.32000 6 CR5 C-0.13000 7 HR5HC 0.13000 7 CR6 C-0.17000 8 HR6HC 0.17000 8 CT2 C-0.21000 9 HT1HC 0.21000 9 CT3 C-0.0900010 CT4 CH3 0.0900010 CT5 C 0.5800011 OT1 O-0.5800011 NT2NR-0.2200012 HT2 H 0.2200012 CT6 C 0.5400013 OT2 O-0.5400013 part of my *.gro file 2VBTCC1 21 3.221 5.305 1.589 2VBTCC2 22 3.143 5.334 1.460 2VBTCR1 23 3.115 5.221 1.384 2VBTCR2 24 3.196 5.155 1.293 2VBTHR2 25 3.305 5.159 1.298 2VBTCR3 26 3.132 5.074 1.200 2VBTHR3 27 3.198 5.003 1.151 2VBTCR4 28 2.995 5.068 1.175 2VBTCT1 29 2.948 5.023 1.052 2VBTNT1 30 3.028 5.038 0.928 2VBTCR5 31 2.919 5.144 1.263 2VBTHR5 32 2.810 5.142 1.268 2VBTCR6 33 2.977 5.208 1.372 2VBTHR6 34
RE: [gmx-users] ErrorBox was shifted at least 10 times. Please see log-file
Hi, In 3.3 position restraints and NPT can also cause trouble when the amount of scaling is large. In 4.0 there is the new refcoord_scaling option that allows scaling of the position restraint reference coordinates or their COM. We would also like to have such a scaling for frozen atoms, but that is not implemented yet. Berk Date: Fri, 17 Oct 2008 07:57:34 -0400 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: Re: [gmx-users] ErrorBox was shifted at least 10 times. Please see log-file CC: gmx-users@gromacs.org There are several potential problems all combined into one. As has been reported on the list, applying freezegrps, constraints, and pressure coupling all at the same time do not mix well. The best bet is to turn off the pressure coupling if you're set on using freezegrps. Otherwise, use position restraints if you require NPT. -Justin vivek sharma wrote: Hi justin, thanks for your response. following is the .mdp file pasted.. _ title = trp_drg warnings= 10 cpp = /lib/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 250 ; total 5000.0 ps. nstcomm = 1 nstxout = 25000 ; output coordinates every 0.5 ps nstvout = 10 ; output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 energygrps_excl = freeze freeze freeze SOL ! To remove computation of interactions between the frozen groups with surroundings (i.e. the solvent, SOL) fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.10.1 0.1 tc_grps = proteinsol NDP ref_t = 300300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ; Non-equilibrium MD stuff freezegrps = freeze freezedim= Y Y Y With Thanks, Vivek 2008/10/17 Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] vivek sharma wrote: Hi Tehre, i am running a job by keeping a part of molecule freeze by using the .mdp option What is your entire .mdp file? -Justin __ energygrps_excl= Terminal Terminal Terminal SOL ! To remove computation of nonbonding interactions between the frozen groups with each other and surroundings (i.e. the solvent, SOL) freezegrps = Terminal ! Index group to freeze freezedim = Y Y Y ! Freeze this group in all directions, x, y, and z ___ where frreze is a group mentioned in the index file... During the run the job is being terminated with the following error . __ Step 1 Warning: pressure scaling more than 1%, mu: -3.51079e+22 -3.51079e+22 -3.51079e+22 --- Program mdrun_d, VERSION 3.3.3 Source code file: ns.c, line: 258 Fatal error: Box was shifted at least 10 times. Please see log-file. --- Error on node 0, will try to stop all the nodes Halting parallel program mdrun_d on CPU 0 out of 24 srun: error: n216: task0: Aborted srun: Terminating job __ Can somebody give an insight in the problem for figuring out the probable cause of the error. PS::Before the run I mentioned the boxsize in editconf as -box 7.5 5 6 , to keep the size of box and number of solvent optimum. Does it have anything to do with the mentioned error ? Looking for suggestions.. with thanks, Vivek
[gmx-users] Problem building a new polymer using pdb2gmx....
Dear David (van der Spoel) Thank you for your time. Firstly: I don't need to add any H atom to my polymer. All atoms that I need are in the rtp topology file. So I did not change the hdb file. Using this command (as you suggested in the last message): pdb2gmx -ignh -ter -f polymer.gro -p top Below I extracted the main differences with the previous pdb2gmx error: Processing chain 1 (239 atoms, 14 residues) Fatal error: Atom O in residue VBT 2 not found in rtp entry with 24 atoms while sorting atoms Evidently, pdb2gmx is doing something funny with my polymer, because it found 239 atoms in my gro file, when it really contains 309. Without the option -ignh (as I did it before) it found the correct number of atoms (309). Finally it also found the atom O in my gro files, which (again) it doesn't really exist. What is pdb2gmx doing? I don't understand what I am doing wrong. Any suggestion will be appreciated. Sergio -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs-4.0 error in grompp
Hello, While I'm trying to use the grompp command I get this error : Program grompp, VERSION 4.0 Source code file: topio.c, line: 415 Fatal error: Syntax error - File topol.top, line 4 Last line read: ' [ system ]' Invalid order for directive system I do not get this error in version 3.3.3 or 3.3.2 though. Any thought? Thank you, Nikos __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs-4.0 error in grompp
Claus Valka wrote: Hello, While I'm trying to use the grompp command I get this error : Program grompp, VERSION 4.0 Source code file: topio.c, line: 415 Fatal error: Syntax error - File topol.top, line 4 Last line read: ' [ system ]' Invalid order for directive system I do not get this error in version 3.3.3 or 3.3.2 though. Any thought? Are you sure it is not a problem with the file? If it is reproducible you can submit a bugzilla. Thank you, Nikos __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem building a new polymer using pdb2gmx....
Alberto Sergio Garay wrote: Dear David (van der Spoel) Thank you for your time. Firstly: I don't need to add any H atom to my polymer. All atoms that I need are in the rtp topology file. So I did not change the hdb file. Using this command (as you suggested in the last message): pdb2gmx -ignh -ter -f polymer.gro -p top Below I extracted the main differences with the previous pdb2gmx error: Processing chain 1 (239 atoms, 14 residues) Fatal error: Atom O in residue VBT 2 not found in rtp entry with 24 atoms while sorting atoms This still looks like it is doing something to your termini, or you could have an error in the rtp file. Can you try to make a minimal system and post it to the list? Evidently, pdb2gmx is doing something funny with my polymer, because it found 239 atoms in my gro file, when it really contains 309. Without the option -ignh (as I did it before) it found the correct number of atoms (309). Finally it also found the atom O in my gro files, which (again) it doesn't really exist. What is pdb2gmx doing? I don't understand what I am doing wrong. Any suggestion will be appreciated. Sergio -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs4: minimization hangs
Dear Gromacs Users, When I run a steepest descent minimization with the parallel version of mdrun in Gromacs 4, it runs to completion (all 1000 steps), but does not exit. See below for the tail end of the log file (notice there are not timings and the usual Gromacs quote at the end). The serial version of the Gromacs 4 mdrun runs this minimization fine and exits as it should. I did not have this issue with the Gromacs4rc3 parallel mdrun. Do you know what might be going wrong? I've attached the min.mdp and min.tpr files. Best regards, Lillian Tail end of log file: Step Time Lambda 1000 1000.00.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.75995e+011.01358e+025.12660e+001.82811e+022.18810e+02 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 8.24670e+021.97157e+04 -9.79168e+02 -1.44989e+05 -1.75892e+04 Potential Pressure (bar) -1.42482e+051.42736e+04 min.mdp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs4: minimization hangs
Lillian Chong wrote: Dear Gromacs Users, When I run a steepest descent minimization with the parallel version of mdrun in Gromacs 4, it runs to completion (all 1000 steps), but does not exit. See below for the tail end of the log file (notice there are not timings and the usual Gromacs quote at the end). The serial version of the Gromacs 4 mdrun runs this minimization fine and exits as it should. I did not have this issue with the Gromacs4rc3 parallel mdrun. Do you know what might be going wrong? Which mpi version are you using? I've attached the min.mdp and min.tpr files. Best regards, Lillian Tail end of log file: Step Time Lambda 1000 1000.00.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.75995e+011.01358e+025.12660e+001.82811e+022.18810e+02 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 8.24670e+021.97157e+04 -9.79168e+02 -1.44989e+05 -1.75892e+04 Potential Pressure (bar) -1.42482e+051.42736e+04 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs4: minimization hangs
I ran the following for the minimization using mpich2: mpiexec -n 8 mdrun_mpi -s min.tpr -c min.gro -o min.trr -g min.log -e min.edr On Fri, Oct 17, 2008 at 12:36 PM, David van der Spoel [EMAIL PROTECTED] wrote: Lillian Chong wrote: Dear Gromacs Users, When I run a steepest descent minimization with the parallel version of mdrun in Gromacs 4, it runs to completion (all 1000 steps), but does not exit. See below for the tail end of the log file (notice there are not timings and the usual Gromacs quote at the end). The serial version of the Gromacs 4 mdrun runs this minimization fine and exits as it should. I did not have this issue with the Gromacs4rc3 parallel mdrun. Do you know what might be going wrong? Which mpi version are you using? I've attached the min.mdp and min.tpr files. Best regards, Lillian Tail end of log file: Step Time Lambda 1000 1000.00.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.75995e+011.01358e+025.12660e+001.82811e+022.18810e+02 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 8.24670e+021.97157e+04 -9.79168e+02 -1.44989e+05 -1.75892e+04 Potential Pressure (bar) -1.42482e+051.42736e+04 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Lillian T. Chong Assistant Professor Department of Chemistry University of Pittsburgh 219 Parkman Avenue Pittsburgh, PA 15260 (412) 624-6026 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs4: minimization hangs
Lillian Chong wrote: I ran the following for the minimization using mpich2: mpiexec -n 8 mdrun_mpi -s min.tpr -c min.gro -o min.trr -g min.log -e min.edr And does it work on fewer processors? In particular on one processor? If so please submit a bugzilla. On Fri, Oct 17, 2008 at 12:36 PM, David van der Spoel [EMAIL PROTECTED] wrote: Lillian Chong wrote: Dear Gromacs Users, When I run a steepest descent minimization with the parallel version of mdrun in Gromacs 4, it runs to completion (all 1000 steps), but does not exit. See below for the tail end of the log file (notice there are not timings and the usual Gromacs quote at the end). The serial version of the Gromacs 4 mdrun runs this minimization fine and exits as it should. I did not have this issue with the Gromacs4rc3 parallel mdrun. Do you know what might be going wrong? Which mpi version are you using? I've attached the min.mdp and min.tpr files. Best regards, Lillian Tail end of log file: Step Time Lambda 1000 1000.00.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.75995e+011.01358e+025.12660e+001.82811e+022.18810e+02 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 8.24670e+021.97157e+04 -9.79168e+02 -1.44989e+05 -1.75892e+04 Potential Pressure (bar) -1.42482e+051.42736e+04 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] implicit solvent in gromacs 4.0?
Hi, I was curious to know whether gromacs 4.0 supports implicit solvent simulation or not. If not, is there any possibility that the implicit solvent model will be implemented in near future ? Thanks Jagannath Mondal Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Using MPI gromacs with CONDOR
Hi, all, I was wondering if there was anyone out there that has successfully used Gromacs, MPI, and CONDOR. One thing that would be particularly useful would be submit scripts. I have installed MPI on my own account, but I haven't figured out how to use MPI with condor. I would appreciate your help. Best wishes, Art ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem building a new polymer using pdb2gmx ....
Dear David (van der Spoel) Thank you for help again! I'm sending a part of my gro input file, which includes the first 2 residues. The VBT 2 is the one which pdb2gmx complains about: pdb2gmx -f polymer.gro -ter -ignh -p top Processing chain 1 (239 atoms, 14 residues) Fatal error: Atom O in residue VBT 2 not found in rtp entry with 24 atoms while sorting atoms Generated by trjconv : 14 TEQ-VBT 1:1 t= .0 309 1TQLCTL1 3.058 5.402 1.733 1TQLCC22 3.144 5.276 1.717 1TQLCR13 3.225 5.235 1.822 1TQLCR24 3.184 5.124 1.894 1TQLHR25 3.092 5.069 1.874 1TQLCR36 3.257 5.086 2.006 1TQLHR37 3.237 4.993 2.060 1TQLCR48 3.373 5.150 2.048 1TQLCR59 3.414 5.263 1.977 1TQLHR5 10 3.510 5.311 1.994 1TQLCR6 11 3.337 5.303 1.869 1TQLHR6 12 3.370 5.401 1.832 1TQLCN4 13 3.439 5.090 2.154 1TQL N 14 3.558 5.089 2.242 1TQLCN1 15 3.575 5.230 2.281 1TQLCN2 16 3.664 5.062 2.144 1TQLCN3 17 3.522 4.977 2.330 1TQLCE1 18 3.523 5.373 2.263 1TQLCE2 19 3.817 5.054 2.153 1TQLCE3 20 3.588 4.905 2.448 2VBTCC1 21 3.221 5.305 1.589 2VBTCC2 22 3.143 5.334 1.460 2VBTCR1 23 3.115 5.221 1.384 2VBTCR2 24 3.196 5.155 1.293 2VBTHR2 25 3.305 5.159 1.298 2VBTCR3 26 3.132 5.074 1.200 2VBTHR3 27 3.198 5.003 1.151 2VBTCR4 28 2.995 5.068 1.175 2VBTCT1 29 2.948 5.023 1.052 2VBTNT1 30 3.028 5.038 0.928 2VBTCR5 31 2.919 5.144 1.263 2VBTHR5 32 2.810 5.142 1.268 2VBTCR6 33 2.977 5.208 1.372 2VBTHR6 34 2.916 5.232 1.459 2VBTCT2 35 3.070 4.916 0.874 2VBTHT1 36 3.009 4.827 0.860 2VBTCT3 37 3.190 4.911 0.804 2VBTCT4 38 3.245 4.779 0.750 2VBTCT5 39 3.264 5.027 0.784 2VBTOT1 40 3.364 5.030 0.712 Below it is a part of the rtp file which includes the VBT building block: [ VBT ] [ atoms ] ; name type charge chargegroup CC1 CH2 0.0 1 CC2 CH1 0.12000 2 CR1 C-0.12000 3 CR2 C-0.14000 4 HR2HC 0.14000 4 CR3 C-0.08000 5 HR3HC 0.08000 5 CR4 C-0.05000 6 CT1 CH2 0.37000 6 NT1NR-0.32000 6 CR5 C-0.13000 7 HR5HC 0.13000 7 CR6 C-0.17000 8 HR6HC 0.17000 8 CT2 C-0.21000 9 HT1HC 0.21000 9 CT3 C-0.0900010 CT4 CH3 0.0900010 CT5 C 0.5800011 OT1 O-0.5800011 NT2NR-0.2200012 HT2 H 0.2200012 CT6 C 0.5400013 OT2 O-0.5400013 ; [ bonds ] ; atom1 atom2 b0 kb CC2 +CC1gb_27 CC1 CC2gb_27 CC2 CR1gb_15 CR1 CR2gb_16 CR2 CR3gb_16 CR3 CR4gb_16 CR4 CR5gb_16 CR5 CR6gb_16 CR6 CR1gb_16 CR2 HR2gb_3 CR3 HR3gb_3 CR5 HR5gb_3 CR6 HR6gb_3 CR4 CT1gb_15 CT1 NT1gb_23 NT1 CT2gb_17 CT2 HT1gb_3 CT2 CT3gb_16 CT3 CT4gb_27 CT3 CT5gb_16 CT5 OT1gb_5 CT5 NT2gb_17 NT2 HT2gb_2 NT2 CT6gb_17 CT6 OT2gb_5 CT6 NT1gb_17 [ angles ] ; aiajak gromos type -CC2 CC1 CC2ga_15 CC1 CC2 +CC1ga_15 CR1 CC2 +CC1ga_15 CC1 CC2 CR1ga_15 CC2 CR1 CR2ga_25 CC2 CR1 CR6ga_25 CR1 CR2 CR3ga_27 CR2 CR3 CR4ga_27 CR3 CR4 CR5ga_27 CR4 CR5 CR6ga_27 CR5 CR6 CR1ga_27 CR6 CR1 CR2ga_27 CR1 CR2 HR2ga_25 HR2 CR2 CR3ga_25 CR2 CR3 HR3ga_25 HR3 CR3 CR4ga_25 CR4 CR5 HR5ga_25 HR5 CR5 CR6ga_25 CR5 CR6 HR6ga_25 HR6 CR6 CR1ga_25 CR3 CR4 CT1ga_25 CR5 CR4 CT1ga_25 CR4 CT1 NT1ga_8 CT1 NT1 CT2ga_27 CT1 NT1 CT6ga_27 NT1 CT2 HT1ga_25 NT1 CT2 CT3ga_27 NT1 CT6 OT2ga_27 NT1 CT6 NT2ga_27 HT1 CT2 CT3ga_25 CT2 CT3 CT4ga_27 CT2 CT3 CT5ga_27 CT4 CT3 CT5ga_27 CT3 CT5 OT1ga_27 CT3 CT5 NT2ga_27 OT1 CT5 NT2ga_27 CT5 NT2 HT2ga_25 CT6 NT2 HT2ga_25 CT5 NT2 CT6ga_27 NT2 CT6 OT2ga_27 CT6 NT1 CT2ga_27 -CCE CC2 +CC1ga_15 -CCE CC2 CR1ga_15 ; [ impropers ] ; aiajakal gromos type CC2 CC1 CR1 +CC1gi_2 ; tymine
Re: [gmx-users] Problem building a new polymer using pdb2gmx ....
Alberto Sergio Garay wrote: Dear David (van der Spoel) Thank you for help again! I'm sending a part of my gro input file, which includes the first 2 residues. The VBT 2 is the one which pdb2gmx complains about: try renaming your OT1 to OX1 or something like this. pdb2gmx might think it is an O-terminal (as you have in proteins) pdb2gmx -f polymer.gro -ter -ignh -p top Processing chain 1 (239 atoms, 14 residues) Fatal error: Atom O in residue VBT 2 not found in rtp entry with 24 atoms while sorting atoms Generated by trjconv : 14 TEQ-VBT 1:1 t= .0 309 1TQLCTL1 3.058 5.402 1.733 1TQLCC22 3.144 5.276 1.717 1TQLCR13 3.225 5.235 1.822 1TQLCR24 3.184 5.124 1.894 1TQLHR25 3.092 5.069 1.874 1TQLCR36 3.257 5.086 2.006 1TQLHR37 3.237 4.993 2.060 1TQLCR48 3.373 5.150 2.048 1TQLCR59 3.414 5.263 1.977 1TQLHR5 10 3.510 5.311 1.994 1TQLCR6 11 3.337 5.303 1.869 1TQLHR6 12 3.370 5.401 1.832 1TQLCN4 13 3.439 5.090 2.154 1TQL N 14 3.558 5.089 2.242 1TQLCN1 15 3.575 5.230 2.281 1TQLCN2 16 3.664 5.062 2.144 1TQLCN3 17 3.522 4.977 2.330 1TQLCE1 18 3.523 5.373 2.263 1TQLCE2 19 3.817 5.054 2.153 1TQLCE3 20 3.588 4.905 2.448 2VBTCC1 21 3.221 5.305 1.589 2VBTCC2 22 3.143 5.334 1.460 2VBTCR1 23 3.115 5.221 1.384 2VBTCR2 24 3.196 5.155 1.293 2VBTHR2 25 3.305 5.159 1.298 2VBTCR3 26 3.132 5.074 1.200 2VBTHR3 27 3.198 5.003 1.151 2VBTCR4 28 2.995 5.068 1.175 2VBTCT1 29 2.948 5.023 1.052 2VBTNT1 30 3.028 5.038 0.928 2VBTCR5 31 2.919 5.144 1.263 2VBTHR5 32 2.810 5.142 1.268 2VBTCR6 33 2.977 5.208 1.372 2VBTHR6 34 2.916 5.232 1.459 2VBTCT2 35 3.070 4.916 0.874 2VBTHT1 36 3.009 4.827 0.860 2VBTCT3 37 3.190 4.911 0.804 2VBTCT4 38 3.245 4.779 0.750 2VBTCT5 39 3.264 5.027 0.784 2VBTOT1 40 3.364 5.030 0.712 Below it is a part of the rtp file which includes the VBT building block: [ VBT ] [ atoms ] ; name type charge chargegroup CC1 CH2 0.0 1 CC2 CH1 0.12000 2 CR1 C-0.12000 3 CR2 C-0.14000 4 HR2HC 0.14000 4 CR3 C-0.08000 5 HR3HC 0.08000 5 CR4 C-0.05000 6 CT1 CH2 0.37000 6 NT1NR-0.32000 6 CR5 C-0.13000 7 HR5HC 0.13000 7 CR6 C-0.17000 8 HR6HC 0.17000 8 CT2 C-0.21000 9 HT1HC 0.21000 9 CT3 C-0.0900010 CT4 CH3 0.0900010 CT5 C 0.5800011 OT1 O-0.5800011 NT2NR-0.2200012 HT2 H 0.2200012 CT6 C 0.5400013 OT2 O-0.5400013 ; [ bonds ] ; atom1 atom2 b0 kb CC2 +CC1gb_27 CC1 CC2gb_27 CC2 CR1gb_15 CR1 CR2gb_16 CR2 CR3gb_16 CR3 CR4gb_16 CR4 CR5gb_16 CR5 CR6gb_16 CR6 CR1gb_16 CR2 HR2gb_3 CR3 HR3gb_3 CR5 HR5gb_3 CR6 HR6gb_3 CR4 CT1gb_15 CT1 NT1gb_23 NT1 CT2gb_17 CT2 HT1gb_3 CT2 CT3gb_16 CT3 CT4gb_27 CT3 CT5gb_16 CT5 OT1gb_5 CT5 NT2gb_17 NT2 HT2gb_2 NT2 CT6gb_17 CT6 OT2gb_5 CT6 NT1gb_17 [ angles ] ; aiajak gromos type -CC2 CC1 CC2ga_15 CC1 CC2 +CC1ga_15 CR1 CC2 +CC1ga_15 CC1 CC2 CR1ga_15 CC2 CR1 CR2ga_25 CC2 CR1 CR6ga_25 CR1 CR2 CR3ga_27 CR2 CR3 CR4ga_27 CR3 CR4 CR5ga_27 CR4 CR5 CR6ga_27 CR5 CR6 CR1ga_27 CR6 CR1 CR2ga_27 CR1 CR2 HR2ga_25 HR2 CR2 CR3ga_25 CR2 CR3 HR3ga_25 HR3 CR3 CR4ga_25 CR4 CR5 HR5ga_25 HR5 CR5 CR6ga_25 CR5 CR6 HR6ga_25 HR6 CR6 CR1ga_25 CR3 CR4 CT1ga_25 CR5 CR4 CT1ga_25 CR4 CT1 NT1ga_8 CT1 NT1 CT2ga_27 CT1 NT1 CT6ga_27 NT1 CT2 HT1ga_25 NT1 CT2 CT3ga_27 NT1 CT6 OT2ga_27 NT1 CT6 NT2ga_27 HT1 CT2 CT3ga_25 CT2 CT3 CT4ga_27 CT2 CT3 CT5ga_27 CT4 CT3 CT5ga_27 CT3 CT5 OT1ga_27 CT3 CT5 NT2ga_27 OT1 CT5 NT2ga_27 CT5 NT2 HT2ga_25 CT6 NT2 HT2ga_25 CT5 NT2 CT6ga_27 NT2 CT6 OT2ga_27 CT6 NT1 CT2
[gmx-users] Problem building a new polymer using pdb2gmx ....
Dear David I renamed the atom OT1 to OX1 in the gro and rtp files but pdb2gmx still gives me the same error: Processing chain 1 (239 atoms, 14 residues) There are 7 donors and 13 acceptors There are 0 hydrogen bonds --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom O in residue VBT 2 not found in rtp entry with 24 atoms while sorting atoms. It is strange that it found 14 residues (which it is correct) but only 239 atoms (the system has 309 atoms) so it seems that pdb2gmx would have taken out all the H atoms of the system. What are the steps that pdb2gmx follows when it works on a molecule? I will be working on it. Thank you in advance for helping me. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] segmentation fault after first header line is printed
Hello,
I compiled GROMACS version 4.0 on an AMD Opteron, running
Red Hat Linux (RHEL4), with the Portland Group compilers,
v. 7.2. The compilation appears to work fine, with the
following procedure:
export CPPFLAGS=-I/usr/local/fftw-3.1.2/include
export LDFLAGS=-L/usr/local/fftw-3.1.2/lib
export CC=pgcc
export F77=pgf77
export LIBS=-L/usr/X11R6/lib64
Configure with the options:
--prefix=/usr/local/gromacs-4.0
--enable-double --enable-shared
Then I edited 1 line in the libtool file generated by
configure:
replaced:
hardcode_libdir_flag_spec=\${wl}--rpath \${wl}\$libdir
by:
hardcode_libdir_flag_spec=-R\$libdir
The reason for this last step is that pgcc does not
recognize the --rpath option. The equivalent option
is -R.
Then
make
make install
worked fine.
Then I did
source /usr/local/gromacs-4.0/bin/GMXRC
If I run any GROMACS binaries after this, by
calling the name itself, e.g.
grompp_d -h
The program outputs a header line
:-) G R O M A C S (-:
and then I get a segmentation fault. And similarly
for other commands, such as mdrun_d, pdb2gmx_d, etc.
However, if I invoke the program with the full
path, e.g.
/usr/local/gromacs-4.0/bin/grompp_d -h
then it is fine. I did an strace on both
commands (without and with the full path)
and it appears that the segmentation fault
comes from the binary trying to open a file
whose name is my environment PATH compounded
many times until the filename is too long.
Interestingly, when I compiled gromacs with
gcc 3.4.6, both ways of invoking the binaries
(with or without the full path) work fine.
Compilation of v.3.3.3 using the PGI compilers
resulted in the same problem (that is, invoking
a binary without the full path generates a
segmentation fault).
I would really like to use gromacs compiled with
the PGI compilers, and be able to invoke the binaries
without the full path.
I would appreciate any ideas how to get this problem
resolved.
Thank you very much,
Shan-Ho
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[gmx-users] Gromacs 4.0 and threads
Hi folks, I have a question that has already been discussed before about other versions. I would like to know if Gromacs 4.0 has a multi-thread implementation. I downloaded and compiled this release with the commands: $ ./configure --enable-threads $ make # make install However, when i perform the command mdrun with option '-nt' is shown the next message: Fatal error: GROMACS compiled without threads support - can only use one thread Regards, Ricardo Rios ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem building a new polymer using pdb2gmx ....
Alberto Sergio Garay wrote: Dear David I renamed the atom OT1 to OX1 in the gro and rtp files but pdb2gmx still gives me the same error: Processing chain 1 (239 atoms, 14 residues) There are 7 donors and 13 acceptors There are 0 hydrogen bonds --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom O in residue VBT 2 not found in rtp entry with 24 atoms while sorting atoms. It is strange that it found 14 residues (which it is correct) but only 239 atoms (the system has 309 atoms) so it seems that pdb2gmx would have taken out all the H atoms of the system. What are the steps that pdb2gmx follows when it works on a molecule? I will be working on it. Thank you in advance for helping me. If you use the -ignh flag the you need to recreate hydrogens using the hydrogen database, If not, then all names in the coordinate file need to match exactly the rtp file. pdb2gmx also renames atoms according to the table in xlateat.dat. You may want to generate a file in your working directory called xlateat.dat which contains just a single zero on the first line. In this way no atom renaming is done. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs 4.0 and threads
Ricardo Rios wrote: Hi folks, I have a question that has already been discussed before about other versions. I would like to know if Gromacs 4.0 has a multi-thread implementation. I downloaded and compiled this release with the commands: $ ./configure --enable-threads $ make # make install However, when i perform the command mdrun with option '-nt' is shown the next message: Fatal error: GROMACS compiled without threads support - can only use one thread There is no thread support. Sorry. Regards, Ricardo Rios ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Blue Gene Compile - GROMACS 4
Mike Hanby wrote: Howdy, I'm looking at compiling Gromacs 4 for the Blue Gene/L and am stuck at the compilation of the prerequisite FFTW 3.1.3. If anyone out there has successfully cross compiled FFTW and Gromacs for the Blue Gene, would you mind sharing your settings used to run the ./configure scripts? I'm getting cannot compute sizeof (unsigned int) which tells me I'm not giving it enough information for the cross compilation. There's two key components: using the BG/L cross compilers (blrts_xlc and blrts_xlf) and letting configure know that you are using cross compilers, so that its tests are constructed using successful compilation, not successful execution. I've successfully used #!/bin/bash CFLAGS=-O5 -qbgl -qarch=440d -qcache=level=1:type=i:size=32:line=32:assoc=64:cost=8 -qcache=level=1:type=d:size=32:line=32:assoc=64:cost=8 -qcache=level=2:type=c:size=4096:line=128:assoc=8:cost=40 -qnoautoconfig -qfloat=norngchk -qhot -qignerrno ./configure CC=blrts_xlc --host=powerpc --build=ppc64 Note that some of those compiler flags are probably redundant, and you should read up on whether you actually want them all. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: implicit solvent in gromacs 4.0?
Depending on how you want to implement the solvent, you can do it now with tabulated potentials. I am moving a project I was doing in another MD package to GROMACS 4.0 that simulates CG lipid bilayers in an implicit solvent according to the following paper. I. R. Cooke and M. Deserno, Journal of Chemical Physics 123, 224710 (2005). -Matt - Matthew Hoopes Biophysics Graduate Group University of California, Davis [EMAIL PROTECTED] 530-752-6452 - jagannath mondal wrote: Hi, I was curious to know whether gromacs 4.0 supports implicit solvent simulation or not. If not, is there any possibility that the implicit solvent model will be implemented in near future ? No, 4.1 or 4.2. Thanks Jagannath Mondal Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Simulation of a protein confined in a box
As you may have seen in the GROMACS 4.0 manual, Walls can only be used with pbc=xy so its more of a floor/ceiling. You still may want a solution beyond the feature mentioned in chapter 7. Particle based realizations for walls may be a bit more work but very doable. See the following paper. Chenyue Xing and Roland Faller J. Phys. Chem. B, 112 (23), 7086-7094, 2008. -Matt -- Message: 3 Date: Sat, 11 Oct 2008 10:41:39 -0400 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Simulation of a protein confined in a box To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Lee Soin wrote: This seems to me a very complicated realization. Why doesn't GROMACS provide an easy way for wall simulation? How about reading manual section 7.3.20 Walls in the Gromacs-4.0 manual? I think that would be what you're after. -Justin 2008/10/11 Omer Markovitch [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Oh, I didn't read carefully. My suggestion would be, perhaps, to physically put atoms on the sides of the box (possibly, fill each side completely), and to place on them very high repulsion. You might want to freeze them up, and exclude their self interactions from the energy calculation. Good guess Suman. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Possibly what he is interested in is a system WITHOUT PBC? I don't think with PBC the system is really confined, since there is no true wall to reflect the colliding molecules. Thus to study the effect of real confinement, it is necessary to remove PBC and impose reflective boundary conditions. I am only guessing! :) --Suman. ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Double precision gives infinite force while single doesn't
Hi! When I'm using double precision calculations, for instance minimization with mdrun_d, I receive infinite forces on the 1 atom each time. But running simple mdrun with quite the same parameters results in normal minimization. I've compiled source code of gromacs-3.3.3, gromacs-4.0 and i always have this problem. Maybe there's some hints for compiling double precision version in Mandriva 2008? Thank you, Alexey Zeifman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ffamber99 topologies for ligand
How do I create topology files for a ligand when using ffamber99 in gromacs? Thank you Fabrício Bracht ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
