Re: [gmx-users] Re: Energy Drift in Gromacs 4.0
Ilya Chorny wrote: Ok, I got it. Set electrostatics to PME-switch. Made rcoulomb-switch .1 less than rcoulomb and set rlist accordingly and now I am conserving energy. Yipee!!! It did not make sense to me that the system had to be fully relaxed to conserve energy. It should conserve energy energy as long as it has been minimized and has no major clashes. This is correct, provided T and P coupling are turned off. Thanks, Ilya On Wed, Mar 11, 2009 at 7:38 PM, Ilya Chorny icho...@gmail.com mailto:icho...@gmail.com wrote: If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE simulation they should counter balance. I am leaking K.E. somewhere. I reran with a relaxed P.E(t) and saw the same behavior. This is happening both at 2 and 4 fs so its not a time step issue. Any thoughts? I thought it might be COM removal so I turned it off to no avail. Any chance one of the Gromacs people can give me the mdp file from the DHFR simulation in the 4.0 paper. On Tue, Mar 10, 2009 at 10:21 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Ilya Chorny wrote: Forgot column labels on energies. Average RMSD Fluct. Drift Tot-Drift 2 fs time step Total Energy46497.2 36445.6 2630.7 -148.833-148833 4 fs time step Total Energy41580.8 37693.42856.08 -130.198-130198 On Tue, Mar 10, 2009 at 7:17 PM, Ilya Chorny icho...@gmail.com mailto:icho...@gmail.com mailto:icho...@gmail.com mailto:icho...@gmail.com wrote: Hello All, I am trying to run some calibration calculations with 2/4 fs time steps. I am trying to reproduce the results in the Gromacs 4.0 paper on a protein/water (not the same protein) system with ~100K atoms. I ran 1 ns simulation in the NVE ensemble. My mdp params are shown below. Topolgy was created using -vsite h. My system has 218441 degrees of freedom according to GMXDUMP. My P.E. energy is ~ -1E5 and has not full relaxed after 1ns but is close. 2 fs time step Total Energy46497.2 36445.62630.7 -148.833-148833 4 fs time step Total Energy41580.8 37693.4 2856.08 -130.198-130198 Drift (kt/ns) 2fs/4fs = .34/.29 The drift seems to be much larger for both the 2fs and 4fs time steps then in the paper. Do I have a clear bug in my params? Should I wait till the system fully relaxes before doing the drift calculation? You should definitely equilibrate the system before trying to measure energy drift. I suggest doing so in NPT to fix your density and temperature, then switching to NVE, wait a bit, and only then start to collect your data. coulombtype = PME rcoulomb = 1.0 fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1.e-04 I would think the ewald_rtol value used in the paper was 1e-5, but it is unfortunately not stated. The different numbers will lead to different costs and accuracies for the direct and FFT parts of the PME algorithm. rcoulomb, fourier_whatever, pme_order and ewald_rtol are all relevant if you're trying to reproduce results. Mark ___ 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ilya Chorny Ph.D. -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] viscosity calculation using g_energy (3.3.3)
JMandumpal wrote: Dear GROMACS users, As explained in the manual ( page 139, section 6.5/3.3.3) I would like to calculate viscosity of my system ( water) using g_energy. I opted(40 Mu-X ) from the g-energy selection. But the unit written on the Y axis of the corresponding xvg file is (kJ mol\S-1\N). I think GROMACS uses SI unit , which is Pa-Second in the case of viscosity. Then why is this discrepancy.? Or did I make any mistake? Mu is the dipole (in Debye). The units of these things are incorrect for everything that is not an energy. This will be fixed in the next gmx version. g_energy -h tells you what to do: g_energy -f ener -vis viscosity --I give the command on the prompt: g-energy -f ener.edr - o viscosity.xvg ; then chose option 40 ( Mu-X). system details: ** My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds at 150K, the ensemble is NPT. The version I am using is 3.3.3 regards, Jes Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715...@middle5/2705639_2677138/2680796/1?PARTNER=3OAS_QUERY=null ___ 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 gmx-users-requ...@gromacs.org. 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. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Questions about urea.itp
Hello! Can the GROMACS topology file urea.itp be used with the OPLS force field? In urea.itp there are two sets of parameters, separated by #ifdef directives. Which set should be used? Thanks! -- 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Questions about urea.itp
Lee Soin wrote: Hello! Can the GROMACS topology file urea.itp be used with the OPLS force field? In urea.itp there are two sets of parameters, separated by #ifdef directives. Which set should be used? Neither. Check the literature. Thanks! -- 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 gmx-users-requ...@gromacs.org. 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. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Broken trr-file
Mark Abraham wrote: Justin A. Lemkul wrote: Hansjoerg Jerabek wrote: Dear Mark! At first: thanks for your reply. The log file has been witten correctly, and gmxcheck gives me the following warning: Checking file ketamine.t2.trr trn version: GMX_trn_file (double precision) Reading frame 0 time 43500.000 # Atoms 25400 Reading frame 4 time 43520.000 Warning at frame 4: coordinates for atom 21839 are large (3.04738e+35) Warning at frame 4: coordinates for atom 21839 are large (2.16053e+185) --- Program gmxcheck_d, VERSION 4.0.3 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- Is it somehow possible to manually remove the corrupt frame from the binary trr-file? I'm asking this because I can't afford to re-run the simulation, since it would take about 3 weeks. trjconv-b 0 -e 3 You will have to sacrifice everything after frame 3 then (since frame 4 is corrupted). Judging by the timeframe of the simulation, that is probably a substantial amount of data. Perhaps you can restart from a checkpoint file, depending on how often those were written, to collect the rest of your data. ... and next time, plan to save yourself data suitable for a restart every few compute hours or so! There's some general information here, but the detail was written for GROMACS 3.3.x. http://wiki.gromacs.org/index.php/Doing_Restarts Mark ... thank you for your advices. since it was impossible to edit the trr-file with any of the gromacs application, I used a hex-editor and a small c++-application to cut the broken frames out. best regards hansjoerg ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)
David, Thanks for the quick reply. Indeed I did as what you suggested- g_energy -f water.edr -vis test.xvg The output file created includes three columns. 1. time ( ps) 2. shear viscosity (3) I assume it is bulk viscosity. It seems, the unit given is cp. ( 1cp= 1* 10¯3 Pascal Second). The bulk viscosity of water at 300 K is approximately 0.7 cp. But the value ( Bulk viscosity) I got from the program gives me 100 pa-s, an increase of two order of magnitude. I wonder whether I have done anything wrong while specifying the frequency of saving energy file. I have saved the energy file in every 2ps. Isn´t that enough for a simple system like water? OR should I have to save trajectories in every 5fs as suggested by one in a previous post. I post the first 20 lines of the output file. --- # This file was created Thu Mar 12 16:20:09 2009 # by the following command: # g_energy -f water.edr -vis test.xvg # # g_energy is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @title Bulk Viscosity @xaxis label Time (ps) @yaxis label \8h\4 (cp) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Shear @ s1 legend Bulk 1.99203 9.6633 96.3893 3.98406 11.1625 98.1365 5.9761 12.6631 99.838 7.96813 13.4652 101.366 9.96016 13.7012 100.249 - regards, Jes On Thu, 12 Mar 2009 David van der Spoel wrote : JMandumpal wrote: Dear GROMACS users, As explained in the manual ( page 139, section 6.5/3.3.3) I would like to calculate viscosity of my system ( water) using g_energy. I opted(40 Mu-X ) from the g-energy selection. But the unit written on the Y axis of the corresponding xvg file is (kJ mol\S-1\N). I think GROMACS uses SI unit , which is Pa-Second in the case of viscosity. Then why is this discrepancy.? Or did I make any mistake? Mu is the dipole (in Debye). The units of these things are incorrect for everything that is not an energy. This will be fixed in the next gmx version. g_energy -h tells you what to do: g_energy -f ener -vis viscosity --I give the command on the prompt: g-energy -f ener.edr - o viscosity.xvg ; then chose option 40 ( Mu-X). system details: ** My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds at 150K, the ensemble is NPT. The version I am using is 3.3.3 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about the restart of the mdrun
Hello, I have a problem when I restrat of mdrun (Gromacs 4.0) using the following command: mdrun -deffnm Asp -cpi -append. The errors like this: eading checkpoint file Asp_md.cpt generated: Wed Mar 11 19:16:24 2009 Build time mismatch, current program: Thu Mar 5 17:52:53 CET 2009 checkpoint file: Fri Jan 30 17:05:24 CET 2009 #PP-nodes mismatch, current program: 2 checkpoint file: 1 Gromacs binary or parallel settings not identical to previous run. Continuation still works, but is not guaranteed to be binary identical. --- Program mdrun, VERSION 4.0.3 Source code file: checkpoint.c, line: 1238 Fatal error: Truncation of file Asp_md.trr failed. --- Anybody has some suggestions? ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Energy Drift in Gromacs 4.0
Even if a system is not well equilibrated (but not so far from equilibrium) ,energy should be conserved in NVE ensemble. Try to lower the nstlist from 10 to 1 i.e. renew every time the neighbourlist. In systems I have studied, that is the key that improve much more energy conservation. It works even without switching of VdW potential. Luca Dre Gaetani Message: 1 Date: Thu, 12 Mar 2009 13:59:11 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Re: Energy Drift in Gromacs 4.0 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 49b87a7f.30...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Ilya Chorny wrote: If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE simulation they should counter balance. I am leaking K.E. somewhere. I reran with a relaxed P.E(t) and saw the same behavior. This is happening both at 2 and 4 fs so its not a time step issue. Any thoughts? I thought it might be COM removal so I turned it off to no avail. going down is seriously unhelpful. I told you you needed to equilibrate before measuring such things. If you want people to take your problem seriously, you'll need to announce that you have equilibrated and for how long and in what ensembles, etc. If you're having a problem, you need to demonstrate what areas you feel are not causing it. We're not your family doctor who will ask a pile of questions to find out the problem :-) 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Karplus parameterization
Dears, Anyone knows which parameterization of the Karplus equation is implemented in g_chi ? Best, XAvier. XAvier Periole MD-group University of Groningen The Netherlands ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Karplus parameterization
XAvier Periole wrote:
Dears,
Anyone knows which parameterization of the Karplus equation
is implemented in g_chi ?
Hm, I'm surprised to see this isn't in the source code with a
please_cite call. My bad, this is at least one of them.
@Article{ Vuister93,
author = G. W. Vuister and A. Bax,
title =Quantitative {J} Correlation: A New Approach for
Measuring Homonuclear Three-Bond
{J(H$^N$-H$^{\alpha}$)} Coupling Constants in
{$^{15}$N}-Enriched Proteins,
journal = BTjacs,
year = 1993,
volume = 115,
pages =7772-
}
Smith, L.J., Sutcliffe, M.J., Redfield, C., and Dobson, C.M. 1991.
Analysis of φ and χ1 torsion angles for hen lysozyme in solution
from 1H NMR spin–spin coupling constants. Biochemistry, 30:
986–996.
@Article{ LSmith96,
author = L. J. Smith and K. A. Bolin and H. Schwalbe and
M. W. Mac{A}rthur and J. M. Thornton and
C. M. Dobson,
title =Analysis of Main Chain Torsion Angles in Proteins:
Prediction of {NMR} Coupling Constants for Native
and Random Coil Conformations,
journal = BTjmb,
year = 1996,
volume = 255,
pages =494-506
}
Best,
XAvier.
XAvier Periole
MD-group
University of Groningen
The Netherlands
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--
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.
sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se
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RE: [gmx-users] viscosity calculation using g_energy (3.3.3)
Hi, This is a very inefficient method for determining the viscosity. Also you need really perfect pressure fluctuations: NVT, shifted potentials, probably even double precision. There was a mail about this recently. There are better methods, have a look at: http://dx.doi.org/10.1063/1.1421362 Berk Date: Thu, 12 Mar 2009 07:39:52 + From: jesb...@rediffmail.com To: gmx-users@gromacs.org Subject: Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3) CC: David, Thanks for the quick reply. Indeed I did as what you suggested- g_energy -f water.edr -vis test.xvg The output file created includes three columns. 1. time ( ps) 2. shear viscosity (3) I assume it is bulk viscosity. It seems, the unit given is cp. ( 1cp= 1* 10¯3 Pascal Second). The bulk viscosity of water at 300 K is approximately 0.7 cp. But the value ( Bulk viscosity) I got from the program gives me 100 pa-s, an increase of two order of magnitude. I wonder whether I have done anything wrong while specifying the frequency of saving energy file. I have saved the energy file in every 2ps. Isn´t that enough for a simple system like water? OR should I have to save trajectories in every 5fs as suggested by one in a previous post. I post the first 20 lines of the output file. --- # This file was created Thu Mar 12 16:20:09 2009 # by the following command: # g_energy -f water.edr -vis test.xvg # # g_energy is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @title Bulk Viscosity @xaxis label Time (ps) @yaxis label \8h\4 (cp) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Shear @ s1 legend Bulk 1.99203 9.6633 96.3893 3.98406 11.1625 98.1365 5.9761 12.6631 99.838 7.96813 13.4652 101.366 9.96016 13.7012 100.249 - regards, Jes On Thu, 12 Mar 2009 David van der Spoel wrote : JMandumpal wrote: Dear GROMACS users, As explained in the manual ( page 139, section 6.5/3.3.3) I would like to calculate viscosity of my system ( water) using g_energy. I opted(40 Mu-X ) from the g-energy selection. But the unit written on the Y axis of the corresponding xvg file is (kJ mol\S-1\N). I think GROMACS uses SI unit , which is Pa-Second in the case of viscosity. Then why is this discrepancy.? Or did I make any mistake? Mu is the dipole (in Debye). The units of these things are incorrect for everything that is not an energy. This will be fixed in the next gmx version. g_energy -h tells you what to do: g_energy -f ener -vis viscosity --I give the command on the prompt: g-energy -f ener.edr - o viscosity.xvg ; then chose option 40 ( Mu-X). system details: ** My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds at 150K, the ensemble is NPT. The version I am using is 3.3.3 _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Re: Energy Drift in Gromacs 4.0
Hi, Everything depends completely on how much drift you are talking about. There will always be energy drift, it is just a question how much. In general shifted potentials will be cheaper (and lead to less energy drift) than setting nstlist to 1, but for most purposes a bit of energy drift is no problem. Berk Date: Thu, 12 Mar 2009 10:55:47 +0100 From: degaet...@dcci.unipi.it To: gmx-users@gromacs.org Subject: [gmx-users] Re: Energy Drift in Gromacs 4.0 Even if a system is not well equilibrated (but not so far from equilibrium) ,energy should be conserved in NVE ensemble. Try to lower the nstlist from 10 to 1 i.e. renew every time the neighbourlist. In systems I have studied, that is the key that improve much more energy conservation. It works even without switching of VdW potential. Luca Dre Gaetani Message: 1 Date: Thu, 12 Mar 2009 13:59:11 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Re: Energy Drift in Gromacs 4.0 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 49b87a7f.30...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Ilya Chorny wrote: If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE simulation they should counter balance. I am leaking K.E. somewhere. I reran with a relaxed P.E(t) and saw the same behavior. This is happening both at 2 and 4 fs so its not a time step issue. Any thoughts? I thought it might be COM removal so I turned it off to no avail. going down is seriously unhelpful. I told you you needed to equilibrate before measuring such things. If you want people to take your problem seriously, you'll need to announce that you have equilibrated and for how long and in what ensembles, etc. If you're having a problem, you need to demonstrate what areas you feel are not causing it. We're not your family doctor who will ask a pile of questions to find out the problem :-) 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to carry out rigid body
Hi everyone, I want to peform CG-MDs with gromacs. In my system, there are some rigid bodies which are composed by hundreds of LJ atoms. Atoms of each rigid body move together in LJ water solution. How can I deal with it? Any suggestion is appreciated. Thanks in advance. -- wende ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to carry out rigid body
In the case of Martini(CG)-derived protein simulations we use an elastic network to connect the backbone (C-alpha) beads. This allows to control the conformation and dynamics of the protein. We parameterized this EN to reproduce atomistic simulations and observed that with a cutoff of 0.8/0.9 nm and a force constant of 500 kJ/mol/nm2 the CG-protein could reproduce structural (rmsd) and dynamical (rmsf and large amplitude collective motion) properties. That might help you, although I am not sure what your objects are. XAvier. On Mar 12, 2009, at 2:47 PM, lammps lammps wrote: Hi everyone, I want to peform CG-MDs with gromacs. In my system, there are some rigid bodies which are composed by hundreds of LJ atoms. Atoms of each rigid body move together in LJ water solution. How can I deal with it? Any suggestion is appreciated. Thanks in advance. -- wende ___ 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Minimization not converging
Hi, I think that my minimization are not running long enough. I've been following the parameters in tutorials but it seems like they all die at 34 steps I've been using these tutorials https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf http://md.chem.rug.nl/education/mdcourse/MDpract.html Its been the same case for me regardless to whether I use Windows or Linux platforms. Are there settings I can use to make the simulation minimize longer or is this case where I need to have double precision version? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Minimization not converging
I should have included some output Step= 32, Dmax= 2.4e-06 nm, Epot= -1.03223e+05 Fmax= 3.87326e+06, atom= 25439 Step= 33, Dmax= 1.2e-06 nm, Epot= -1.03222e+05 Fmax= 3.87334e+06, atom= 25439 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax 10. Potential Energy = -1.4354568e+06 Maximum force = 6.9535597e+10 on atom 25439 Norm of force = 4.5592896e+08 More details here. http://www.hydrogenathome.org/result.php?resultid=1291344 On Thu, Mar 12, 2009 at 10:59 AM, Jack Shultz jshu...@hydrogenathome.org wrote: Hi, I think that my minimization are not running long enough. I've been following the parameters in tutorials but it seems like they all die at 34 steps I've been using these tutorials https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf http://md.chem.rug.nl/education/mdcourse/MDpract.html Its been the same case for me regardless to whether I use Windows or Linux platforms. Are there settings I can use to make the simulation minimize longer or is this case where I need to have double precision version? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Minimization not converging
Jack Shultz wrote: I should have included some output Step= 32, Dmax= 2.4e-06 nm, Epot= -1.03223e+05 Fmax= 3.87326e+06, atom= 25439 Step= 33, Dmax= 1.2e-06 nm, Epot= -1.03222e+05 Fmax= 3.87334e+06, atom= 25439 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax 10. Potential Energy = -1.4354568e+06 Maximum force = 6.9535597e+10 on atom 25439 Norm of force = 4.5592896e+08 More details here. http://www.hydrogenathome.org/result.php?resultid=1291344 From your pdb2gmx output, it looks like you have some lousy starting geometry in whatever structure you're processing: http://wiki.gromacs.org/index.php/Errors#Long_bonds_and.2For_missing_atoms Try to run EM on that structure before solvating (i.e., in vacuo) , because you probably have lots of steric clashes with the solvent arising because of improper protein geometry. -Justin On Thu, Mar 12, 2009 at 10:59 AM, Jack Shultz jshu...@hydrogenathome.org wrote: Hi, I think that my minimization are not running long enough. I've been following the parameters in tutorials but it seems like they all die at 34 steps I've been using these tutorials https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf http://md.chem.rug.nl/education/mdcourse/MDpract.html Its been the same case for me regardless to whether I use Windows or Linux platforms. Are there settings I can use to make the simulation minimize longer or is this case where I need to have double precision version? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb files
Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA ? Thanks in advance You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). --- On Sat, 3/7/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: gurbulako...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, March 7, 2009, 9:28 AM oguz gurbulak wrote: Dear All, I want to use packmol pdb files that includes one or two different types of molecules. And I seached Gromacs manuals, tutorials and mail archives in order to have enough information about using packmol pdb files in Gromacs. But I couldn't find any information. So Could you please give me the information about this ? How can I use a packmol pdb file for oplsaa and gromacs united-atom force field in generating .gro and .top files for md simulations? You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). Do not use the Gromacs force field (ffgmx); it is deprecated and should not be used for new simulations. Use a newer Gromos96 variant. You can get Gromos96-compatible topologies from the PRODRG 2.5 server, but be warned that the charges and charge groups assigned by PRODRG are often inconsistent and unsatisfactory, requiring manual alteration and validation. Summary: 1. Create .itp files for each molecule type individually. 2. Construct a .top yourself, which would be as simple as: #include ffoplsaa.itp #include molecule_A.itp #include molecule_B.itp #include spc.itp #include ions.itp [ system ] packmol system [ molecules ] Molecule_A N Molecule_B N SOL N (then whatever ions you need, if any) -Justin Sincerely ___ gmx-users mailing list 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Variance in ED
Hi all, perhaps a silly question but i didn't find the correct way to calculate the variance explained by each eigenvec in ED analysis. Could someone point me out to a correct tool/option to use. I'm using gmx v3.3. Many thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials
Hello again. It's pretty clear now for me thanks. I still have a little problem due to the unphysical trend of the BKS potentials for r -- 0 : it goes to minus infinity. The atoms can thus collide in case of a high temperature (providing them enough velocity to overcome the barrier) and I get the following error which I suppose is connected to this problem : Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 8 ] Practically, at ambient temperatures of the order of 300 K, it doesn't happen but I want to anneal first at 5000 K to get a melt SiO2 and then quench it to 300 K. The standard procedure to avoid particle colliding is to add a hard repulsive part acting only on short distances. Is it possible to add a repulsive part on short distances only (something like Vrep(r)=a*(r-r0)^4 with r0 being the distance at which the barrier is at its maximum) and how could I do it ? The potential energy should then be V=Vrep(r) for r r0 and V=V_BKS(r) for r r0. If it's not possible analytically, I assume I should use a user specified potential function by making a table.xvg file with the x, f(x), f'(x), etc ... as it is mentioned in the manual (p133 and p148) ? David Waroquiers - PhD Student Université Catholique de Louvain Laboratoire de Physico-Chimie et de Physique des Matériaux European Theoretical Spectroscopy Facility Mark Abraham wrote: David Waroquiers wrote: Hello I'm trying to simulate amorphous SiO2 with the use of the BKS potentials (van Beest, B. W. H.; Kramer, G. J. van Santen, R. A. - Phys. Rev. Lett., American Physical Society, 1990, 64, 1955-1958). According to these potentials, I should use the Buckingham potentials with user-defined parameters plus a coulomb part with user-defined charges for each atom type. I don't need any other forcefield from GROMACS. When I try to preprocess my topology file and get the .tpr binary file in order to start the simulation, I get the following message in the terminal : processing topology... Generated 0 of the 3 non-bonded parameter combinations Excluding 0 bonded neighbours molecule type 'O' Excluding 0 bonded neighbours molecule type 'Si' I don't understand why my non-bonded parameters aren't generated ... Generation refers to the process described in (probably) chapter 4 of the manual where all possible pairwise interactions between a set of atom types are calculated from generic parameters characteristic of the two atom types involved (see your [atomtypes] entries). An alternative is to describe the pairwise interactions specifically, as you have done. Thus GROMACS didn't need to generate any, and reports this fact. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb files
Will I write two .rtp files for two different molecules ? or Will I write one rtp file that includes all parameters of these two molecules ? And how can I use the rtp file when creating the input files ( .gro and .top ) ? Thanks in advance --- On Thu, 3/12/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, March 12, 2009, 12:11 PM oguz gurbulak wrote: Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA ? You're stuck either writing an .rtp entry for use with pdb2gmx, or writing the .itp yourself. -Justin Thanks in advance You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). --- On *Sat, 3/7/09, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: gurbulako...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, March 7, 2009, 9:28 AM oguz gurbulak wrote: Dear All, I want to use packmol pdb files that includes one or two different types of molecules. And I seached Gromacs manuals, tutorials and mail archives in order to have enough information about using packmol pdb files in Gromacs. But I couldn't find any information. So Could you please give me the information about this ? How can I use a packmol pdb file for oplsaa and gromacs united-atom force field in generating .gro and .top files for md simulations? You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). Do not use the Gromacs force field (ffgmx); it is deprecated and should not be used for new simulations. Use a newer Gromos96 variant. You can get Gromos96-compatible topologies from the PRODRG 2.5 server, but be warned that the charges and charge groups assigned by PRODRG are often inconsistent and unsatisfactory, requiring manual alteration and validation. Summary: 1. Create .itp files for each molecule type individually. 2. Construct a .top yourself, which would be as simple as: #include ffoplsaa.itp #include molecule_A.itp #include molecule_B.itp #include spc.itp #include ions.itp [ system ] packmol system [ molecules ] Molecule_A N Molecule_B N SOL N (then whatever ions you need, if any) -Justin Sincerely ___ gmx-users mailing list gmx-users@gromacs.org /mc/compose?to=gmx-us...@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 gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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] problems with gmxtest.pl
Dear users and developers of gromacs, although running the tests is straight forward some advice how to interpret the results would be helpful. If a test ends with Testing xyz . . . PASSED but check mdp file differences and 'diff' of the mdp files shows a differenet file header only everything seems to be fine. Is this right? One of the 45 pdb2gmx tests fails. Presumably it is that one which puts its files into: pdb2gmx/pdb-6pti/ffencads/none/spc The potential energies of the other tests in ener.log deviate from those in reference_s.log. Is there a rule of thumb how small the deviations should be in order to be tolerable? Best regards Bernhard Bandow -- - Dr. Bernhard BandowPhone: +49 511 762 794727 Leibniz Universitaet Hannover FAX: +49 511 762 3003 RRZN / HLRNEmail: ban...@rrzn.uni-hannover.de Schlosswender Str. 5 D-30159 Hannover http://www.rrzn.uni-hannover.de/ Germanyhttp://www.hlrn.de/ - ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb files
oguz gurbulak wrote: Will I write two .rtp files for two different molecules ? or Will I write one rtp file that includes all parameters of these two molecules ? And how can I use the rtp file when creating the input files ( .gro and .top ) ? Read the manual, section 5.6.1. -Justin Thanks in advance --- On *Thu, 3/12/09, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, March 12, 2009, 12:11 PM oguz gurbulak wrote: Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA ? You're stuck either writing an .rtp entry for use with pdb2gmx, or writing the .itp yourself. -Justin Thanks in advance You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). --- On *Sat, 3/7/09, Justin A. Lemkul /jalem...@vt.edu /mc/compose?to=jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu /mc/compose?to=jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: gurbulako...@yahoo.com /mc/compose?to=gurbulako...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org Date: Saturday, March 7, 2009, 9:28 AM oguz gurbulak wrote: Dear All, I want to use packmol pdb files that includes one or two different types of molecules. And I seached Gromacs manuals, tutorials and mail archives in order to have enough information about using packmol pdb files in Gromacs. But I couldn't find any information. So Could you please give me the information about this ? How can I use a packmol pdb file for oplsaa and gromacs united-atom force field in generating .gro and .top files for md simulations? You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). Do not use the Gromacs force field (ffgmx); it is deprecated and should not be used for new simulations. Use a newer Gromos96 variant. You can get Gromos96-compatible topologies from the PRODRG 2.5 server, but be warned that the charges and charge groups assigned by PRODRG are often inconsistent and unsatisfactory, requiring manual alteration and validation. Summary: 1. Create .itp files for each molecule type individually. 2. Construct a .top yourself, which would be as simple as: #include ffoplsaa.itp #include molecule_A.itp #include molecule_B.itp #include spc.itp #include ions.itp [ system ] packmol system [ molecules ] Molecule_AN Molecule_BN SOL N (then whatever ions you need, if any) -Justin Sincerely ___ gmx-users mailing listgmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org /mc/compose?to=gmx-us...@gromacs.org /mc/compose?to=gmx-us...@gromacs.org
Re: [gmx-users] Variance in ED
Hi Andrea, The variance associated with an eigenvector is the eigenvalue. The sum of the eigenvalues captures the total variance. Accordingly, dividing an eigenvalue by the sum of all eigenvalues gives the part of the total variance explained by the eigenvector. Cheers, Tsjerk On Thu, Mar 12, 2009 at 5:36 PM, andrea carotti and...@chimfarm.unipg.it wrote: Hi all, perhaps a silly question but i didn't find the correct way to calculate the variance explained by each eigenvec in ED analysis. Could someone point me out to a correct tool/option to use. I'm using gmx v3.3. Many thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar ___ gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in energy minimization
Hi everyone, I am trying to run a simulation on a xray structure that has 15 residues missing. I have made the topology file accordingly. But after energy minimization, the residues between which the portion is missing, got connected. I tried an energy minimization with all-bonds constraint, but that i guess did not do it properly. This is the last part of the minimization run Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up ccpox_em.trr to ./#ccpox_em.trr.1# Back Off! I just backed up ccpox_b4pr.pdb to ./#ccpox_b4pr.pdb.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = -2.2785961e+05 Maximum force = 5.1547680e+08 on atom 1004 Norm of force = 8.2600877e+08 My question is how can I run a simulation on these structure keeping that part as it is? Thanking you in advance. Abhik Abhik Mukhopadhyay Departamento Química / Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa , 2829-516 Caparica, Portugal Mob. 00351912991251 http://xtal.dq.fct.unl.pt/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] removal of COM
Hello Users I am trying to measure the drift of molecules in the system. When I ran the simulation, the removal of center-of-mass of the whole system took place at every step. From the mailing list, I've found that removal of COM works by making the velocity of the COM to be zero by subtracting the velocity from every particle velocity. It would be very grateful if you can help me to make two points clear; 1) Would the magnitude to be subtracted from every particle velocity be the same (or different depending on the mass of the particle)? 2) Could removal of COM make one type of molecule move in an opposite direction of the other molecules that move in one direction to keep maintain the COM of the system at its original position? Thank you in advance Sunjoo ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in energy minimization
Abhik Mukhopadhyay wrote: Hi everyone, I am trying to run a simulation on a xray structure that has 15 residues missing. I have made the topology file accordingly. But after energy minimization, the residues between which the portion is missing, got connected. I tried an energy minimization with all-bonds constraint, but that i guess did not do it properly. This is the last part of the minimization run When you created the topology, did pdb2gmx add a bond between the residues flanking the missing residues? What was your pdb2gmx command line? If you are sure that the missing residues will not influence the dynamics (think carefully!), then read in the manual about distance restraints. If you have difficulties implementing these restraints, there are dozens of posts in the list archive that should guide you in how to use them. -Justin Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up ccpox_em.trr to ./#ccpox_em.trr.1# Back Off! I just backed up ccpox_b4pr.pdb to ./#ccpox_b4pr.pdb.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = -2.2785961e+05 Maximum force = 5.1547680e+08 on atom 1004 Norm of force = 8.2600877e+08 My question is how can I run a simulation on these structure keeping that part as it is? Thanking you in advance. Abhik *Abhik Mukhopadhyay * Departamento Química / Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa , 2829-516 Caparica, Portugal Mob. 00351912991251 http://xtal.dq.fct.unl.pt/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Reducing Size of Data
Hi, I was wondering if there are any ways to reduce the amount of data produce or compact it better. On some of my runs mdruns I ran out of the default disk space BOINC allocated for my file system to run this analysis. If I use the -compact flag, does that affect the size of the trajectory files? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reducing Size of Data
Jack Shultz wrote: Hi, I was wondering if there are any ways to reduce the amount of data produce or compact it better. On some of my runs mdruns I ran out of the default disk space BOINC allocated for my file system to run this analysis. If I use the -compact flag, does that affect the size of the trajectory files? Increase nstxout, nstvout, and nstxtcout. That will reduce the size of the .trr and .xtc, which are likely the largest files that you will be writing. If you want to decrease the .xtc file even more, specify xtc_grps. If the .log and .edr files get out of hand, adjust nstlog and nstenergy. The -compact flag only affects the .log file, and is set by default. -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reducing Size of Data
Jack Shultz wrote: Hi, I was wondering if there are any ways to reduce the amount of data produce or compact it better. On some of my runs mdruns I ran out of the default disk space BOINC allocated for my file system to run this analysis. If I use the -compact flag, does that affect the size of the trajectory files? http://wiki.gromacs.org/index.php/Using_Trajectory_Information#Reducing_Trajectory_Storage_Volume 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] removal of COM
Sun Joo Lee wrote: Hello Users I am trying to measure the drift of molecules in the system. When I ran the simulation, the removal of center-of-mass of the whole system took place at every step. From the mailing list, I've found that removal of COM works by making the velocity of the COM to be zero by subtracting the velocity from every particle velocity. It would be very grateful if you can help me to make two points clear; 1) Would the magnitude to be subtracted from every particle velocity be the same (or different depending on the mass of the particle)? The same. The COM is the mass-weighted center of geometry, so COM velocity is already the rate of change of the displacement of the mass-weighted center of geometry. 2) Could removal of COM make one type of molecule move in an opposite direction of the other molecules that move in one direction to keep maintain the COM of the system at its original position? Sure. Consider a system with three particles moving to the left with speed 3 and one particle moving to the left with speed 1. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problems with gmxtest.pl
Dear users and developers of gromacs, despite checking for the usage of the proper version of tests after upgrading to gromacs-4.0.4 the test suite still produces results with the status FAILED. This is the case for some tests in kernel, complex, and pdb2gmx. For example kernel020 fails with /kernel020/checkvir.out containing: LJ-14step 0: -63.1209, step 0: 6.50743 Potentialstep 0: -321.601, step 0: -251.973 Kinetic En. step 0: 15.0135, step 0: 29.0739 Total Energy step 0: -306.588, step 0: -222.899 Temperature step 0: 1.93226, step 0: 3.74185 Pressure (bar) step 0: -3095.37, step 0: -2497.8 Vir-XX step 0: 1127.45, step 0: 1075.85 Vir-XY step 0:63.524, step 0: 21.7767 Vir-XZ step 0: -264.813, step 0: -260.354 Vir-YX step 0: 63.5241, step 0: 21.7771 Vir-YY step 0: 803.252, step 0: 581.703 Vir-ZX step 0: -264.813, step 0: -260.355 Vir-ZZ step 0: 321.207, step 0: 176.573 Any hints to locate the reasons for this behavior are appreciated. Best regards Bernhard Bandow -- - Dr. Bernhard BandowPhone: +49 511 762 794727 Leibniz Universitaet Hannover FAX: +49 511 762 3003 RRZN / HLRNEmail: ban...@rrzn.uni-hannover.de Schlosswender Str. 5 D-30159 Hannover http://www.rrzn.uni-hannover.de/ Germanyhttp://www.hlrn.de/ - ___ 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Force Field - Gromos96
Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96 force field can support All-Atom calculation? (Or does it 'only' support Unified Atom simulation?) Thank you for your care! Sincerely, C Kim ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] free energy coupling/decoupling equivalence
Hello, I have just read an interesting paper suggesting that the reference state in free energy decoupling/coupling simulations should be the one with larger entropy. Lu and Kofke Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling JCP V. 114, N. 17 pp. 7303-7311 (2001). I have seen some mention that: begin quote Ordinarily, one would expect that forward and reverse only are meaningful when you're (a) doing nonequilibrium simulations, or (b) beginning simulations at lambda values from the ending configurations at preceding lambda values. end quote http://www.gromacs.org/pipermail/gmx-users/2008-February/032430.html And now I am confused, since I would have thought that this was an important forward vs. reverse difference, although I may have my terminology wrong here. To put my questions succinctly: 1. In the gromacs implementation, is there any important difference between coupling and decoupling? I avoid the terms forwrad and reverse in order to avoid non-equilibrium or slow-growth connotations. 2. Does soft-core work properly for both LJ coupling and LJ decoupling? I am not clear how mdrun knows whether to soft-core lambda or 1-lambda since it is near the decoupled state that really needs the soft-core, and this could be at lambda or 1-lambda. Background information: I am doing coulomb and LJ separately; LJ only with soft-core; coulomb first in the decoupling. Everything is working fine for me in the decoupling department, but I am now considering switching to coupling as opposed to decoupling based on this Lu 2001 paper and am interested if anybody has some comments. Thank you, Chris. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fwd: Force Field - Gromos96
-- Forwarded message -- From: tree tree@gmail.com Date: Thu, Mar 12, 2009 at 10:09 PM Subject: Force Field - Gromos96 To: gmx-users@gromacs.org Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96 force field can support All-Atom calculation? (Or does it 'only' support Unified Atom simulation?) Thank you for your care! Sincerely, C Kim ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gmx in GPU calculation
Dear all: I am troubled with this problem: when I run mdrun_openm faaia in GPU calculation of gmx, I met the following information: *Back Off! I just backed up md.log to md.log.2* ** *Getting Loaded...* ** *Reading file 1.tpr, VERSION 4.0.3 (single precision)* ** *Note: tpx file_version 58, software version 59* ** *Segmentation fault* What does it mean? How can I run the this simulation? Thanks a lot... Ming ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
