[gmx-users] grommp_md error
Justin A. Lemkul
jalemkul at vt.edu
Tue Jul 13 05:16:19 CEST 2010
Moeed wrote:
> Hello,
>
> Sorry I did not paste the error message part properly. Initially I am
> trying to study PE in vacuum (current box size 30*30*30 nm) and then I
> will solvate the PE with Hexane.
>
>
> NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]:
> The Berendsen thermostat does not generate the correct kinetic energy
> distribution. You might want to consider using the V-rescale thermostat.
>
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
> 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
> Opening library file /chem_soft/gromacs/share/gromacs/top/spc.itp
> Opening library file /chem_soft/gromacs/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'polymer'
> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 300 K
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
> Making dummy/rest group for Acceleration containing 2896 elements
> Making dummy/rest group for Freeze containing 2896 elements
> Making dummy/rest group for Energy Mon. containing 2896 elements
> Making dummy/rest group for VCM containing 2896 elements
> Number of degrees of freedom in T-Coupling group Eth is 5373.22
> Number of degrees of freedom in T-Coupling group EthB is 211.89
> Number of degrees of freedom in T-Coupling group EthE is 211.89
> Making dummy/rest group for User1 containing 2896 elements
> Making dummy/rest group for User2 containing 2896 elements
> Making dummy/rest group for XTC containing 2896 elements
> Making dummy/rest group for Or. Res. Fit containing 2896 elements
> Making dummy/rest group for QMMM containing 2896 elements
> T-Coupling has 3 element(s): Eth EthB EthE
> Energy Mon. has 1 element(s): rest
> Acceleration has 1 element(s): rest
> Freeze has 1 element(s): rest
> User1 has 1 element(s): rest
> User2 has 1 element(s): rest
> VCM has 1 element(s): rest
> XTC has 1 element(s): rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
> writing run input file...
>
> There was 1 note
>
> There was 1 warning
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: gmx_fatal.c, line: 481
>
> Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> -------------------------------------------------------
>
> "My Heart is Just a Muscle In a Cavity" (F. Black)
>
> :-) G R O M A C S (-:
>
> Gromacs Runs One Microsecond At Cannonball Speeds
>
> :-) VERSION 4.0.7 (-:
>
>
> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2008, The GROMACS development team,
> check out http://www.gromacs.org for more information.
>
> This program is free software; you can redistribute it and/or
> modify it under the terms of the GNU General Public License
> as published by the Free Software Foundation; either version 2
> of the License, or (at your option) any later version.
>
> :-) grompp (double precision) (-:
>
> processing topology...
> turning all bonds into constraints...
> Analysing residue names:
> There are: 240 OTHER residues
> There are: 0 PROTEIN residues
> There are: 0 DNA residues
> Analysing Other...
> This run will generate roughly 14 Mb of data
>
> *********************************************************************************************************
> Then I altered the tc groups in mdp file to Polymer and use n option in
> grompp.
>
Do you understand why you're doing this? Or are you just trying to follow some
other advice that's been taken out of context?
> grompp -f md-July11-NPTcompression.mdp -c PE60_b4pr -p PE60.top -o
> PE60_md -n index.ndx >& output.grompp_md
>
> (actually I wanted to what how tc group names are based on? I thought
> they come from residue names, then I changed index file [all] name to
You should read about thermostats in the manual, relevant literature, and
perhaps some textbooks before you do anything else. If you have a single
polymer molecule in vacuum, you do not need any special groups, just "System."
If the reasons for this are unclear to you, stop and read before doing anything
else, or you're going to waste a lot of time.
> [polymer]
> index file:
> [ special ]
> 1 3
> [ Polymer ]
> 1 2 3 4
This index file looks familiar. It serves no purpose to you any more. Please
see the Gromacs manual for the proper use of index groups and what they should
actually contain.
> error:******************************************************************
> WARNING 1 [file md-July11-NPTcompression.mdp, line unknown]:
> Unknown or double left-hand 'rvw-switch' in parameter file
>
This is a simple typo.
<snip>
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: readir.c, line: 1069
>
> Fatal error:
> 358 atoms are not part of any of the T-Coupling groups
> -------------------------------------------------------
>
Apparently, you're coupling 4 atoms and ignoring the rest. Sounds like a
serious problem to me.
> "Rat-tat-tat Ka boom boom" (The Smashing Pumpkins)
>
> :-) G R O M A C S (-:
>
> Glycine aRginine prOline Methionine Alanine Cystine Serine
>
> :-) VERSION 4.0.7 (-:
>
>
> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2008, The GROMACS development team,
> check out http://www.gromacs.org for more information.
>
> This program is free software; you can redistribute it and/or
> modify it under the terms of the GNU General Public License
> as published by the Free Software Foundation; either version 2
> of the License, or (at your option) any later version.
>
> :-) grompp (double precision) (-:
>
> processing topology...
> turning all bonds into constraints...
> ******************************************************************************************************************
> .
>
> 2- I have a question about doing NPT for compressing the system. Can I
> also do NVT for a short time and when the chain has a more realistic
> structure , take that structure and change the volume myself? I am just
> asking for the sake of learning.. This doesnt mean I am not going to do
> follow your advise..
>
Sure, you can do anything you want, just make sure it actually has a purpose
that you can defend.
> 3- Also If I want to find the pressure which gives the size I want, I
> need to wait till the end of simulation to see the volume (eg with
> g_energy) and repeat this to find the desired volume by try and error?
>
Maybe? Ideally, if your parameters for the molecule and your settings in the
.mdp file are reasonable, you should be able to reproduce a true physical model,
within the limitations of the force field.
The better approach might be to simulate under NVT for a while, such that the
chain collapses a bit, then proceed to NPT to equilibrate it to (hopefully) the
proper density, not the other way around.
-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
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