[gmx-users] problem in gmx-users list archive?
Dear administrators of gmx-users list, I would like to report a problem in the gmx-users list archive (or at least in its visualization in the Web site). Starting from 2011, when I search in the archive on the Gromacs web site, I can see that multiple copies of identical messages are reported in the archive. For example, searching the archive using the sentence fixing terminals of protein, I wrote the sentence in the mask, click on search and the system returned with at least 40 identical messages dated 2011-04-21 posted by Taylor Kaplan with the subject PYP Connection. If I choose any of these messages, they are absolutely identical. Apparently, this problem starts from March 2011 (messages older than March are correctly visualized once for each message). Obviously this complicates the consultation of the archive. Could you please fix this problem? Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with a gun is a dead man (Roberto Benigni, about Roberto Saviano) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] simulation of a peptide anchored to a support
On 19/05/2011 7:09 PM, Anna Marabotti wrote: Dear gmx-users, I would like to simulate the conformational behaviour of a peptide covalently anchored to a rigid support with its N- and C-ter. I'm not interested in simulating the support, so I wonder if there is a way to simulate the peptide with its N- and C-ter fixed. Could freezegrps work for this? Probably - but not with NPT. However, a strong position restraint is probably easier. Otherwise (or in addition) could I fix the peptide on one side of the simulation box, in order to avoid the fluctuation of the peptide into the solvent? Not sure what you mean. Finally, do I have to add special constraints/restraints to my molecule? Depends on the strategy. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_msd query
Anirban Ghosh skrev 2011-05-19 11.58: Hi ALL, I am trying to calculate the lateral diffusion coefficient of a protein in a bilayer (CG simulation using MARTINI FF). The simulation length is 5 micro-seconds. I wanted to know based on what should i set the values of -beginfit and -endfit and also the value for -trestart. Is it necessary to set -trestart? Thanks a lot in advance. Regards, Anirban -trestart is in principle not necessary, but will provide better statistics. It will also increase the calculation time. -beginfit and -endfit should be set to exclude non-linear (non-converged) part of the msd plot. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
R: Re: [gmx-users] simulation of a peptide anchored to a support
Dear Mark, thank you for suggestions. I suspected that freezegrps does not work with NPT but I'm not sure that position restraints work with the same final effect. Concerning fixing the peptide on the simulation box, I would like to simulate as much as possible the fact that the peptide is fixed on a rigid support, so I'd like to avoid a peptide that rotates and fluctuates into the simulation box. I wonder if there is a way to fix the peptide like a handle in one of the walls of the box itself (obviously, in the internal part of the box). Thanks a lot to anybody will contribute to the discussion! Anna Date: Thu, 19 May 2011 19:17:20 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] simulation of a peptide anchored to a support To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dd4e020.2080...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 19/05/2011 7:09 PM, Anna Marabotti wrote: Dear gmx-users, I would like to simulate the conformational behaviour of a peptide covalently anchored to a rigid support with its N- and C-ter. I'm not interested in simulating the support, so I wonder if there is a way to simulate the peptide with its N- and C-ter fixed. Could freezegrps work for this? Probably - but not with NPT. However, a strong position restraint is probably easier. Otherwise (or in addition) could I fix the peptide on one side of the simulation box, in order to avoid the fluctuation of the peptide into the solvent? Not sure what you mean. Finally, do I have to add special constraints/restraints to my molecule? Depends on the strategy. Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110519/2a8d564f/a ttachment-0001.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] reg centre of mass in SMD
vidhya sankar wrote: Thank you Dr Justinj, To do SMD should i create centre of mass of my reference (protein) and pull group (ligand)? if i need to create , which tool of gromacs generate to be used .? How to include this center of mass in SMD .mdp files None of this is necessary. Gromacs does all COM calculations internally. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] average trajectory
Dear gromacs users, 1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns). I want to make a distance matrix (*g_mdmat*) for the average trajectory of these 3 runnings. *g_mdmat* gives an average matrix for one trajectory, but I want to get it for the average trajectory. I tried to use *xpm2ps* to get average matrix, but in it I can only combine matrices (not to take an average matrix). Can I get an average matrix, or an average trajectory? -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About -pbc option of trjconv
Hi ALL, I have a long simulation trajectory of 3 micro-seconds of multiple protein monomers in a lipid bilayer. Which -pbc option should be used with trjconv to process the trajectory before carrying out any analysis? I am using -pbc nojump, is it correct? Or should I use -pbc whole? Thanks a lot in advance. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About -pbc option of trjconv
Anirban Ghosh wrote: Hi ALL, I have a long simulation trajectory of 3 micro-seconds of multiple protein monomers in a lipid bilayer. Which -pbc option should be used with trjconv to process the trajectory before carrying out any analysis? I am using -pbc nojump, is it correct? Or should I use -pbc whole? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] average trajectory
Yulian Gavrilov wrote: Dear gromacs users, 1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns). I want to make a distance matrix (*g_mdmat*) for the average trajectory of these 3 runnings. *g_mdmat* gives an average matrix for one trajectory, but I want to get it for the average trajectory. I tried to use *xpm2ps* to get average matrix, but in it I can only combine matrices (not to take an average matrix). Can I get an average matrix, or an average trajectory? I have thought about doing this myself, but have never attempted it. There is no Gromacs tool that will do such operations on .xpm files. The best I could figure would be to write an external script that: 1. Translates the .xpm matrix to numerical values based on the the header information 2. Takes the average at each position in the matrix 3. Writes a new .xpm file -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] average trajectory
Justin A. Lemkul skrev 2011-05-19 14.30: Yulian Gavrilov wrote: Dear gromacs users, 1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns). I want to make a distance matrix (*g_mdmat*) for the average trajectory of these 3 runnings. *g_mdmat* gives an average matrix for one trajectory, but I want to get it for the average trajectory. I tried to use *xpm2ps* to get average matrix, but in it I can only combine matrices (not to take an average matrix). Can I get an average matrix, or an average trajectory? I have thought about doing this myself, but have never attempted it. There is no Gromacs tool that will do such operations on .xpm files. The best I could figure would be to write an external script that: 1. Translates the .xpm matrix to numerical values based on the the header information 2. Takes the average at each position in the matrix 3. Writes a new .xpm file -Justin I remember using imagemagick tools (composite?) to make average matrices from xpm files. I don't remember exacly how I did it though, and it may have required hacking the palette in the xpm files before combining them. Cheers, -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: energy groups in tabulated potentials
Please do not send unsolicited email requesting private help. I am forwarding this to the appropriate forum. On point, I think the examples and explanations given in various manual sections deal with your case. Mark Original Message Subject:energy groups in tabulated potentials Date: Thu, 19 May 2011 14:52:16 +0530 From: sreelakshmi ramesh sree.laks...@research.iiit.ac.in To: mark.abra...@anu.edu.au dear mark, I have the following mdp file for running the tabulated potential.i created two tables one for Na Cl interaction tabel_Na_Cl.xvg.and another table for sovent with na and cl interaction called [table.xvg]( solvent is going to interact with both and na and cl with the same potential).so i have a doubt in writing the format in energygrps in mdp file.can you help me out. title = nacl cpp = /usr/bin/cpp ; the c preprocessor define= -DEFLEXIBLE integrator = md coulombtype = user energygrps = Na Cl Sol # help needed in this line energygrp_table = Na Cl # help needed in this lines as well vdwtype= user -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] average trajectory
Hey,
If you can sum them, the only thing needed afterwards is updating the
color labels. Like per awk (dividing by two):
awk -F\ '/#/{$4=$4/2}1' file.xpm
Cheers,
Tsjerk
On Thu, May 19, 2011 at 2:43 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Justin A. Lemkul skrev 2011-05-19 14.30:
Yulian Gavrilov wrote:
Dear gromacs users,
1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns).
I want to make a distance matrix (*g_mdmat*) for the average trajectory
of these 3 runnings. *g_mdmat* gives an average matrix for one trajectory,
but I want to get it for the average trajectory.
I tried to use *xpm2ps* to get average matrix, but in it I can only
combine matrices (not to take an average matrix).
Can I get an average matrix, or an average trajectory?
I have thought about doing this myself, but have never attempted it.
There is no Gromacs tool that will do such operations on .xpm files. The
best I could figure would be to write an external script that:
1. Translates the .xpm matrix to numerical values based on the the header
information
2. Takes the average at each position in the matrix
3. Writes a new .xpm file
-Justin
I remember using imagemagick tools (composite?) to make average matrices
from xpm files. I don't remember exacly how I did it though, and it may have
required hacking the palette in the xpm files before combining them.
Cheers,
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
gmx-users mailing list gmx-users@gromacs.org
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or send it to gmx-users-requ...@gromacs.org.
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: R: Re: [gmx-users] simulation of a peptide anchored to a support
On 19/05/2011 8:10 PM, Anna Marabotti wrote: Dear Mark, thank you for suggestions. I suspected that freezegrps does not work with NPT but I'm not sure that position restraints work with the same final effect. Concerning fixing the peptide on the simulation box, I would like to simulate as much as possible the fact that the peptide is fixed on a rigid support, so I'd like to avoid a peptide that rotates and fluctuates into the simulation box. I wonder if there is a way to fix the peptide like a handle in one of the walls of the box itself (obviously, in the internal part of the box). If the box is periodic, then there is no wall to it. If the box is not periodic, then you have bigger problems to solve. It sounds to me like you're trying to model something that is not reality. The peptide fixed on a rigid support still interacts with the support and the solvent (e.g. the support generates ordered solvent, which affects the peptide), and any attempt to artificially reduce the degrees of freedom of the simulation runs the risk that you have constructed your observations in advance through choosing your initial conditions. Mark Thanks a lot to anybody will contribute to the discussion! Anna Date: Thu, 19 May 2011 19:17:20 +1000 From: Mark Abrahammark.abra...@anu.edu.au Subject: Re: [gmx-users] simulation of a peptide anchored to a support To: Discussion list for GROMACS usersgmx-users@gromacs.org Message-ID:4dd4e020.2080...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 19/05/2011 7:09 PM, Anna Marabotti wrote: Dear gmx-users, I would like to simulate the conformational behaviour of a peptide covalently anchored to a rigid support with its N- and C-ter. I'm not interested in simulating the support, so I wonder if there is a way to simulate the peptide with its N- and C-ter fixed. Could freezegrps work for this? Probably - but not with NPT. However, a strong position restraint is probably easier. Otherwise (or in addition) could I fix the peptide on one side of the simulation box, in order to avoid the fluctuation of the peptide into the solvent? Not sure what you mean. Finally, do I have to add special constraints/restraints to my molecule? Depends on the strategy. Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110519/2a8d564f/a ttachment-0001.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Manually aborting a simulation
Hi, I have started a lengthy equilibration run, and I just realized that I have one of my parameters set incorrectly in my mdp file. Is there any way that I can manually abort the run? I am using Gromacs 4.5.4 with parallel simulation with MPI and the command: mpirun -machinefile cp -np 8 mdrun -s nvt-pr.tpr -o nvt-pr.trr -c water.pdb -e nvt-pr.edr -g nvt-pr.log Thank you. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Manually aborting a simulation
Andrew DeYoung wrote: Hi, I have started a lengthy equilibration run, and I just realized that I have one of my parameters set incorrectly in my mdp file. Is there any way that I can manually abort the run? I am using Gromacs 4.5.4 with parallel simulation with MPI and the command: mpirun -machinefile cp -np 8 mdrun -s nvt-pr.tpr -o nvt-pr.trr -c water.pdb -e nvt-pr.edr -g nvt-pr.log Use 'ps' to locate the process ID and kill it in the terminal. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] water dimer is gas phase
Hello, I am trying a simulation for water dimer in vaccum (gas phase). Here I run the simulation with following steps This is the .pdb file before energy minimization TITLE S C A M O R G REMARKTHIS IS A SIMULATION BOX CRYST13.0003.0003.000 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 OW WAT 1 0.317 1.494 1.565 1.00 0.00 ATOM 2 HW1 WAT 1 -0.091 2.293 1.258 1.00 0.00 ATOM 3 HW2 WAT 1 -0.144 0.788 1.129 1.00 0.00 ATOM 4 OW WAT 2 3.172 1.515 1.356 1.00 0.00 ATOM 5 HW1 WAT 2 2.224 1.482 1.459 1.00 0.00 ATOM 6 HW2 WAT 2 3.522 1.427 2.231 1.00 0.00 TER ENDMDL I run the energy minimization grompp -f minim-gas.mdp -c dimer.pdb -p dimer.top -o dimer.tpr mdrun -pd -s dimer.tpr -o dimer.trr -c dimer.pdb -e dimer.edr -g dimer.log I got the following file which I could visualize TITLE Protein MODEL1 ATOM 1 OW WAT 1 0.351 1.490 1.592 1.00 0.00 ATOM 2 HW1 WAT 1 -0.106 2.335 1.248 1.00 0.00 ATOM 3 HW2 WAT 1 -0.162 0.750 1.112 1.00 0.00 ATOM 4 OW WAT 2 3.198 1.519 1.321 1.00 0.00 ATOM 5 HW1 WAT 2 2.174 1.481 1.457 1.00 0.00 ATOM 6 HW2 WAT 2 3.544 1.423 2.268 1.00 0.00 TER ENDMDL minim-gas.mdp file title = cpeptide cpp = /usr/bin/cpp constraints = none integrator = steep dt = 0.002; ps ! nsteps = 5 nstlist = 1 coulombtype = cut-off vdwtype = cut-off ns_type = simple rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes pbc = no ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 the I run equlibration grompp -f minim-pr.mdp -c dimer.pdb -p dimer.top -o dimer.tpr mdrun -pd -s dimer.tpr -o dimer.trr -c dimer.pdb -e dimer.edr -g dimer.log I got the following file which I could not visualize TITLE Protein MODEL1 ATOM 1 OW WAT 1-2737.208 974.242-2091.510 1.00 0.00 ATOM 2 HW1 WAT 1-2737.949 973.910-2090.885 1.00 0.00 ATOM 3 HW2 WAT 1-2736.363 974.004-2091.048 1.00 0.00 ATOM 4 OW WAT 22740.655-971.0932094.500 1.00 0.00 ATOM 5 HW1 WAT 22740.852-971.7332093.873 1.00 0.00 ATOM 6 HW2 WAT 22740.420-971.4722095.431 1.00 0.00 TER ENDMDL the equlibration file I used title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001; ps ! nsteps = 100 ; total 1.0 ps. nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = simple comm_mode = none coulombtype = cut-off vdwtype = cut-off rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 298 ; Pressure coupling is on Pcoupl = NO ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 298.0 gen_seed= 173529 Is ther any thing wrong with my mdp files. WHy they is so much change is cooridnates in the .pdb file. I am using gromacs version 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: water dimer is gas phase
the equlibration file I used title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001 ; ps ! nsteps = 100 ; total 1.0 ps. nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = simple comm_mode = none coulombtype = cut-off vdwtype = cut-off rlist = 0.0 rcoulomb = 0.0 rvdw = 0.0 pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 298 ; Pressure coupling is on Pcoupl = NO ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 298.0 gen_seed = 173529 Is ther any thing wrong with my mdp files. WHy they is so much change is cooridnates in the .pdb file. Nilesh: Set periodic conditions. This will restrict the coordinates to small numbers. -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: water dimer is gas phase
if I set pbc=xyz in energy minimization mdp file then I get following error ERROR: can only have neighborlist cut-off zero (=infinite) with coulombtype = Cut-off or coulombtype = User and simple neighborsearch without periodic boundary conditions (pbc = no) and rcoulomb and rvdw set to zero ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. Nilesh On Thu, May 19, 2011 3:57 pm, Vitaly Chaban wrote: the equlibration file I used title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001 ; ps ! nsteps = 100 ; total 1.0 ps. nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = simple comm_mode = none coulombtype = cut-off vdwtype = cut-off rlist = 0.0 rcoulomb = 0.0 rvdw = 0.0 pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 298 ; Pressure coupling is on Pcoupl = NO ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 298.0 gen_seed = 173529 Is ther any thing wrong with my mdp files. WHy they is so much change is cooridnates in the .pdb file. Nilesh: Set periodic conditions. This will restrict the coordinates to small numbers. -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: water dimer is gas phase
Vitaly Chaban wrote: the equlibration file I used title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001; ps ! nsteps = 100 ; total 1.0 ps. nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = simple comm_mode = none coulombtype = cut-off vdwtype = cut-off rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 298 ; Pressure coupling is on Pcoupl = NO ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 298.0 gen_seed= 173529 Is ther any thing wrong with my mdp files. WHy they is so much change is cooridnates in the .pdb file. Nilesh: Set periodic conditions. This will restrict the coordinates to small numbers. For vacuum systems, pbc = no in conjunction with zero cutoffs is correct to obtain a gas-phase system. The system has clearly exploded. To diagnose, I would suggest: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: water dimer is gas phase
For vacuum systems, pbc = no in conjunction with zero cutoffs is correct to obtain a gas-phase system. For reasonably large box, this is the same heck. Nilesh: visualize your system, using VMD or ngmx. The behavior of your molecular cluster during the first ps will provide an answer. Are you sure that your topology is healthy? -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 The system has clearly exploded. To diagnose, I would suggest: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: water dimer is gas phase
Very good. Have you take a moment to define the box in the GRO file? -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 On Thu, May 19, 2011 at 4:05 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: if I set pbc=xyz in energy minimization mdp file then I get following error ERROR: can only have neighborlist cut-off zero (=infinite) with coulombtype = Cut-off or coulombtype = User and simple neighborsearch without periodic boundary conditions (pbc = no) and rcoulomb and rvdw set to zero ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: water dimer is gas phase
Vitaly Chaban wrote: For vacuum systems, pbc = no in conjunction with zero cutoffs is correct to obtain a gas-phase system. For reasonably large box, this is the same heck. Setting a box size and using pbc = xyz precludes the use of infinite cutoffs, which should be the most rigorously correct way to treat this type of system. With PBC, there are long-range effects that should be avoided. Nilesh: visualize your system, using VMD or ngmx. The behavior of your molecular cluster during the first ps will provide an answer. Are you sure that your topology is healthy? I agree with this. The system should be going absolutely haywire :) -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] issue with newest version of martini model
I am getting ab error with the newest version of the martini model in which seq2itp, atom2cg generate structures with a topology mismatch if there are any alanines in the structure 9. mutating out the alanines seems to resolve the problem? are there any bug fixes out there? thanks jeremy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] X-ray Structures
Hi, I have a question about using X-ray PDB files for simulations: 1. Is there any rule of thumb on how good a resolution is required for simulations? I know it has nothing to do with GROMACS. Thanks for your insight. Simon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Manually aborting a simulation
On 20/05/2011 3:45 AM, Justin A. Lemkul wrote: Andrew DeYoung wrote: Hi, I have started a lengthy equilibration run, and I just realized that I have one of my parameters set incorrectly in my mdp file. Is there any way that I can manually abort the run? I am using Gromacs 4.5.4 with parallel simulation with MPI and the command: mpirun -machinefile cp -np 8 mdrun -s nvt-pr.tpr -o nvt-pr.trr -c water.pdb -e nvt-pr.edr -g nvt-pr.log Use 'ps' to locate the process ID and kill it in the terminal. The above command will only still be running if its terminal is still alive, and from that terminal you can use jobs, which will give you a small number associated with all such running processes. Now kill %n will kill it, or fg %n to bring it to the foreground so that Ctrl-C will kill it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] X-ray Structures
On 20/05/2011 7:38 AM, simon sham wrote: Hi, I have a question about using X-ray PDB files for simulations: 1. Is there any rule of thumb on how good a resolution is required for simulations? Not really. The lower the resolution, the more likely that the initial conditions for the simulation are not very reflective of reality. If so, getting the system to equilibrate can be more fiddly. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem during energy minimization
Dear Gmx users, I am trying to do minimization of my system .i have no problem wehen i grompp it but when i do the mdrun its giving me some segmentation error.I had attached the output of grompp and mdrun below.Any suggestions please.Thanks in advance *OUTPUT OF GROMPP* Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Ion' Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 2Ion residues There are: 875 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 5253.00 Largest charge group radii for Van der Waals: 0.039, 0.039 nm Largest charge group radii for Coulomb: 0.085, 0.085 nm This run will generate roughly 7 Mb of data Back Off! I just backed up em.tpr to ./#em.tpr.2# *OUTPUT OF MDRUN* Reading file em.tpr, VERSION 4.5.3 (single precision) Starting 2 threads WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'NA SODIUM ION in water' 1 steps,200.0 ps. step 0: Water molecule starting at atom 2553 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 0: Water molecule starting at atom 2595 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault *EM.MDP* title = nacl cpp = /usr/bin/cpp ; the c preprocessor ;define= -DEFLEXIBLE integrator = md dt = 0.02 ; ps ! nsteps = 1 nstlist = -1 coulombtype = user energygrps = Na Cl Sol energygrp_table = Na Cl vdwtype= user ns_type = grid rlist = 1.4 rcoulomb = 1.0 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 pbc=xyz; ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 regards, sree -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem during energy minimization
sreelakshmi ramesh wrote: Dear Gmx users, I am trying to do minimization of my system .i have no problem wehen i grompp it but when i do the mdrun its giving me some segmentation error.I had attached the output of grompp and mdrun below.Any suggestions please.Thanks in advance *OUTPUT OF GROMPP* Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Ion' Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 2Ion residues There are: 875 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 5253.00 Largest charge group radii for Van der Waals: 0.039, 0.039 nm Largest charge group radii for Coulomb: 0.085, 0.085 nm This run will generate roughly 7 Mb of data Back Off! I just backed up em.tpr to ./#em.tpr.2# *OUTPUT OF MDRUN* Reading file em.tpr, VERSION 4.5.3 (single precision) Starting 2 threads WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential These messages indicate that your tables are severely malformed. I suspect your system is collapsing from an unrealistic physical model. -Justin Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'NA SODIUM ION in water' 1 steps,200.0 ps. step 0: Water molecule starting at atom 2553 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 0: Water molecule starting at atom 2595 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault *EM.MDP* title = nacl cpp = /usr/bin/cpp ; the c preprocessor ;define= -DEFLEXIBLE integrator = md dt = 0.02 ; ps ! nsteps = 1 nstlist = -1 coulombtype = user energygrps = Na Cl Sol energygrp_table = Na Cl vdwtype= user ns_type = grid rlist = 1.4 rcoulomb = 1.0 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 pbc=xyz; ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 regards, sree -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem during energy minimization
hai, to check if my table is correct i just copied the 6-9 table for /share/top to local directory ( to check if the prob is same with any other potential) and grompped it and when i did the mdrun i am still getting the same error.Any suggestions. On Fri, May 20, 2011 at 6:29 AM, Justin A. Lemkul jalem...@vt.edu wrote: sreelakshmi ramesh wrote: Dear Gmx users, I am trying to do minimization of my system .i have no problem wehen i grompp it but when i do the mdrun its giving me some segmentation error.I had attached the output of grompp and mdrun below.Any suggestions please.Thanks in advance *OUTPUT OF GROMPP* Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Ion' Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 2Ion residues There are: 875 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 5253.00 Largest charge group radii for Van der Waals: 0.039, 0.039 nm Largest charge group radii for Coulomb: 0.085, 0.085 nm This run will generate roughly 7 Mb of data Back Off! I just backed up em.tpr to ./#em.tpr.2# *OUTPUT OF MDRUN* Reading file em.tpr, VERSION 4.5.3 (single precision) Starting 2 threads WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential These messages indicate that your tables are severely malformed. I suspect your system is collapsing from an unrealistic physical model. -Justin Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'NA SODIUM ION in water' 1 steps,200.0 ps. step 0: Water molecule starting at atom 2553 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 0: Water molecule starting at atom 2595 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault *EM.MDP* title = nacl cpp = /usr/bin/cpp ; the c preprocessor ;define= -DEFLEXIBLE integrator = md dt = 0.02 ; ps ! nsteps = 1 nstlist = -1 coulombtype = user energygrps = Na Cl Sol energygrp_table = Na Cl vdwtype= user ns_type = grid rlist = 1.4 rcoulomb = 1.0 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 pbc=xyz; ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 regards, sree -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem during energy minimization
1. you're not doing energy minimization as your title suggests, please use a better title: integrator = md 2. generally, when you have a problem it is useful to try to simplify the system (e.g. get rid of those tables) and try to reproduce the problem with the simplest system possible before posting. 3. I know that you commented it out, but the following command looks like a typo or a misunderstanding... perhaps you meant -DFLEXIBLE ? ;define= -DEFLEXIBLE 4. Most relevant to you: This is a little ambitious, don't you think? dt = 0.02 ; ps ! Chris. -- original message -- Dear Gmx users, I am trying to do minimization of my system .i have no problem wehen i grompp it but when i do the mdrun its giving me some segmentation error.I had attached the output of grompp and mdrun below.Any suggestions please.Thanks in advance *OUTPUT OF GROMPP* Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Ion' Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 2Ion residues There are: 875 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 5253.00 Largest charge group radii for Van der Waals: 0.039, 0.039 nm Largest charge group radii for Coulomb: 0.085, 0.085 nm This run will generate roughly 7 Mb of data Back Off! I just backed up em.tpr to ./#em.tpr.2# *OUTPUT OF MDRUN* Reading file em.tpr, VERSION 4.5.3 (single precision) Starting 2 threads WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'NA SODIUM ION in water' 1 steps,200.0 ps. step 0: Water molecule starting at atom 2553 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 0: Water molecule starting at atom 2595 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault *EM.MDP* title = nacl cpp = /usr/bin/cpp ; the c preprocessor ;define= -DEFLEXIBLE integrator = md dt = 0.02 ; ps ! nsteps = 1 nstlist = -1 coulombtype = user energygrps = Na Cl Sol energygrp_table = Na Cl vdwtype= user ns_type = grid rlist = 1.4 rcoulomb = 1.0 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 pbc=xyz; ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 regards, sree -- next part -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
