[gmx-users] using Berger Lipids in gromacs 4.5.3

NG HUI WEN HuiWen.Ng at nottingham.edu.my
Mon Jan 24 15:22:22 CET 2011


Hi Justin,

Thanks for your reply. I am using linux on a cluster remotely. It is made up of Hewlett Packard ProLiant DL160 compute nodes. I didn't see any "._" appearing in my gromos53a6_lipid.ff folder.

Huiwen

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Monday, January 24, 2011 10:14 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3



NG HUI WEN wrote:
> Dear Justin,
> 
> Thanks for pointing out :) much appreciated.
> 
> I tried selecting "1" and the process seemed to stop after the work "Atomtype 1", please see below:
> 
>  pdb2gmx -f  prot_moved.pdb -o prot_pdb2gmx.pdb -p prot.top -ter -asp -his
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>                    GROningen MAchine for Chemical Simulation
> 
>                             :-)  VERSION 4.5.3  (-:
> 
>         Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>       Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, 
>         Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, 
>            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, 
>                 Michael Shirts, Alfons Sijbers, Peter Tieleman,
> 
>                Berk Hess, David van der Spoel, and Erik Lindahl.
> 
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>             Copyright (c) 2001-2010, The GROMACS development team at
>         Uppsala University & The Royal Institute of Technology, Sweden.
>             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.
> 
>                                :-)  pdb2gmx  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f prot_moved.pdb  Input        Structure file: gro g96 pdb tpr
>                                    etc.
>   -o prot_pdb2gmx.pdb  Output       Structure file: gro g96 pdb etc.
>   -p    prot.top  Output       Topology file
>   -i      posre.itp  Output       Include file for topology
>   -n      clean.ndx  Output, Opt. Index file
>   -q      clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.
> 
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    0       Set the nicelevel
> -chainsep    enum   id_or_ter  Condition in PDB files when a new chain and
>                             molecule_type should be started: id_or_ter,
>                             id_and_ter, ter, id or interactive
> -ff          string select  Force field, interactive by default. Use -h for
>                             information.
> -water       enum   select  Water model to use: select, none, spc, spce,
>                             tip3p, tip4p or tip5p
> -[no]inter   bool   no      Set the next 8 options to interactive
> -[no]ss      bool   no      Interactive SS bridge selection
> -[no]ter     bool   yes     Interactive termini selection, iso charged
> -[no]lys     bool   no      Interactive Lysine selection, iso charged
> -[no]arg     bool   no      Interactive Arganine selection, iso charged
> -[no]asp     bool   yes     Interactive Aspartic Acid selection, iso charged
> -[no]glu     bool   no      Interactive Glutamic Acid selection, iso charged
> -[no]gln     bool   no      Interactive Glutamine selection, iso neutral
> -[no]his     bool   yes     Interactive Histidine selection, iso checking
>                             H-bonds
> -angle       real   135     Minimum hydrogen-donor-acceptor angle for a
>                             H-bond (degrees)
> -dist        real   0.3     Maximum donor-acceptor distance for a H-bond (nm)
> -[no]una     bool   no      Select aromatic rings with united CH atoms on
>                             Phenylalanine, Tryptophane and Tyrosine
> -[no]ignh    bool   no      Ignore hydrogen atoms that are in the pdb file
> -[no]missing bool   no      Continue when atoms are missing, dangerous
> -[no]v       bool   no      Be slightly more verbose in messages
> -posrefc     real   1000    Force constant for position restraints
> -vsite       enum   none    Convert atoms to virtual sites: none, hydrogens
>                             or aromatics
> -[no]heavyh  bool   no      Make hydrogen atoms heavy
> -[no]deuterate bool no      Change the mass of hydrogens to 2 amu
> -[no]chargegrp bool yes     Use charge groups in the rtp file
> -[no]cmap    bool   yes     Use cmap torsions (if enabled in the rtp file)
> -[no]renum   bool   no      Renumber the residues consecutively in the output
> -[no]rtpres  bool   no      Use rtp entry names as residue names
> 
> 
> Select the Force Field:
>>From current directory:
>  1: GROMOS96 53A6 force field, extended to include Berger lipid parameters
>>From '/usr/remote/gromacs/4.5.3/share/gromacs/top':
>  2: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
>  3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>  4: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
>  5: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
>  6: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
>  7: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
>  8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>  9: CHARMM27 all-atom force field (with CMAP) - version 2.0
> 10: GROMOS96 43a1 force field
> 11: GROMOS96 43a2 force field (improved alkane dihedrals)
> 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 16: [DEPRECATED] Encad all-atom force field, using full solvent charges
> 17: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
> 18: [DEPRECATED] Gromacs force field (see manual)
> 19: [DEPRECATED] Gromacs force field with hydrogens for NMR
> 1
> 
> Using the Gromos53a6_lipid force field in directory ./gromos53a6_lipid.ff
> 
> Opening force field file ./gromos53a6_lipid.ff/watermodels.dat
> 
> Select the Water Model:
>  1: SPC    simple point charge, recommended
>  2: SPC/E  extended simple point charge
>  3: None
> 1
> Opening force field file ./gromos53a6_lipid.ff/aminoacids.r2b
> Reading prot_moved.pdb...
> Read 4914 atoms
> Analyzing pdb file
> Splitting PDB chains based on TER records or changing chain id.
> There are 1 chains and 0 blocks of water and 310 residues with 4914 atoms
> 
>   chain  #res #atoms
>   1 'X'   310   4914  
> 
> All occupancies are one
> Opening force field file ./gromos53a6_lipid.ff/atomtypes.atp
> Atomtype 1
> 
> Not sure what happened... 
> Since there is an option "1" available now, do I still need the gromos53a6_lipid.ff in my current working directory?
> 

The only reason that option "1" appeared is because it is in the working directory.

What type of machine are you on?  I've had this hang happen on my Mac before, 
due to the presence of ._ files when you copy from a different location.  I've 
disabled that option on my workstation.  Other than that, I have no clue why it 
would stop there.

-Justin

> Thanks a lot!
> 
> HW
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
> Sent: Sunday, January 23, 2011 9:06 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3
> 
> 
> 
> NG HUI WEN wrote:
>> Oops sorry!
>>  
>> I found the mistake...
>>  
>> the topology file should read
>> "gromos53a6_lipid.ff/forcefield.itp" instead of 
>> "gromos53a6.ff/forcefield.itp"
>>  
> 
> You would have gotten this if you had chosen the proper force field with 
> pdb2gmx.  Option 1 (which includes the Berger lipids) is the correct one. 
> Option 14 is the vanilla Gromos96 53a6 force field, which is not what you want.
> 
> -Justin
> 
>> silly me
>>
>> ------------------------------------------------------------------------
>> *From:* gmx-users-bounces at gromacs.org on behalf of NG HUI WEN
>> *Sent:* Sun 1/23/2011 1:40 PM
>> *To:* gmx-users at gromacs.org
>> *Subject:* [gmx-users] using Berger Lipids in gromacs 4.5.3
>>
>> Dear all,
>>  
>> This must be a pretty simple problem but I am stuck nonetheless. I have 
>> been using the lipids from Prof Tieleman's website without any problem 
>> on gromacs 4.0.7.
>>  
>> Now that I've got 4.5.3 installed, I want to try the g_membed tool but 
>> have encountered these problems.
>>  
>> Following Justin's tutorial which gives a good tip on how to deal with 
>> the changes introduced in 4.5.3, these are the things I have done + the 
>> output
>>  
>> 1) gave new names to the modified  itp files from 4.0.7
>> ffG53a6_lipid.itp to forcefield.itp
>> ffG53a6nb_lipid.itp to ffnonbonded.itp
>> ffG53a6bon_lipid.itp to ffbonded.itp
>>  
>> 2) created a folder gromos53a6_lipid.ff in the working directory to 
>> contain the files in (1)
>>  
>> 3) copied aminoacids.c.tdb, aminoacids.n.tdb, aminoacids.hdb, 
>> aminoacids.r2b, aminoacids.rtp, aminoacids.vsd, ff_dumitp, spc.itp, 
>> ions.itp, watermodels.dat from $GMXLIB into the gromos53a6_lipid.ff 
>> folder created in step (2). The created a forcefield.doc as instructed.
>>  
>> 4) created .itp for my protein with pdb2gmx 
>> huiwen3 at magnum <mailto:huiwen3 at magnum> 182% pdb2gmx -f protein_moved.pdb 
>> -o protein_pdb2gmx.pdb -p protein.top -ignh
>>                          :-)  G  R  O  M  A  C  S  (-:
>>                Giant Rising Ordinary Mutants for A Clerical Setup
>>                             :-)  VERSION 4.5.3  (-:
>>         Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>>       Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>>         Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>>            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>>                 Michael Shirts, Alfons Sijbers, Peter Tieleman,
>>                Berk Hess, David van der Spoel, and Erik Lindahl.
>>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>             Copyright (c) 2001-2010, The GROMACS development team at
>>         Uppsala University & The Royal Institute of Technology, Sweden.
>>             check out http://www.gromacs.org <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.
>>                                :-)  pdb2gmx  (-:
>> Option     Filename  Type         Description
>> ------------------------------------------------------------
>>   -f protein_moved.pdb  Input        Structure file: gro g96 pdb tpr etc.
>>   -o protein_pdb2gmx.pdb  Output       Structure file: gro g96 pdb etc.
>>   -p    protein.top  Output       Topology file
>>   -i      posre.itp  Output       Include file for topology
>>   -n      clean.ndx  Output, Opt. Index file
>>   -q      clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.
>> Option       Type   Value   Description
>> ------------------------------------------------------
>> -[no]h       bool   no      Print help info and quit
>> -[no]version bool   no      Print version info and quit
>> -nice        int    0       Set the nicelevel
>> -chainsep    enum   id_or_ter  Condition in PDB files when a new chain and
>>                             molecule_type should be started: id_or_ter,
>>                             id_and_ter, ter, id or interactive
>> -ff          string select  Force field, interactive by default. Use -h for
>>                             information.
>> -water       enum   select  Water model to use: select, none, spc, spce,
>>                             tip3p, tip4p or tip5p
>> -[no]inter   bool   no      Set the next 8 options to interactive
>> -[no]ss      bool   no      Interactive SS bridge selection
>> -[no]ter     bool   no      Interactive termini selection, iso charged
>> -[no]lys     bool   no      Interactive Lysine selection, iso charged
>> -[no]arg     bool   no      Interactive Arganine selection, iso charged
>> -[no]asp     bool   no      Interactive Aspartic Acid selection, iso charged
>> -[no]glu     bool   no      Interactive Glutamic Acid selection, iso charged
>> -[no]gln     bool   no      Interactive Glutamine selection, iso neutral
>> -[no]his     bool   no      Interactive Histidine selection, iso checking
>>                             H-bonds
>> -angle       real   135     Minimum hydrogen-donor-acceptor angle for a
>>                             H-bond (degrees)
>> -dist        real   0.3     Maximum donor-acceptor distance for a H-bond 
>> (nm)
>> -[no]una     bool   no      Select aromatic rings with united CH atoms on
>>                             Phenylalanine, Tryptophane and Tyrosine
>> -[no]ignh    bool   yes     Ignore hydrogen atoms that are in the pdb file
>> -[no]missing bool   no      Continue when atoms are missing, dangerous
>> -[no]v       bool   no      Be slightly more verbose in messages
>> -posrefc     real   1000    Force constant for position restraints
>> -vsite       enum   none    Convert atoms to virtual sites: none, hydrogens
>>                             or aromatics
>> -[no]heavyh  bool   no      Make hydrogen atoms heavy
>> -[no]deuterate bool no      Change the mass of hydrogens to 2 amu
>> -[no]chargegrp bool yes     Use charge groups in the rtp file
>> -[no]cmap    bool   yes     Use cmap torsions (if enabled in the rtp file)
>> -[no]renum   bool   no      Renumber the residues consecutively in the 
>> output
>> -[no]rtpres  bool   no      Use rtp entry names as residue names
>>
>> Select the Force Field:
>>  From current directory:
>>  1: GROMOS96 53A6 force field, extended to include Berger lipid parameters
>>  From '/usr/remote/gromacs/4.5.3/share/gromacs/top':
>>  2: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
>>  3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>>  4: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
>>  5: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
>>  6: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
>>  7: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 
>> 1950-58, 2010)
>>  8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>>  9: CHARMM27 all-atom force field (with CMAP) - version 2.0
>> 10: GROMOS96 43a1 force field
>> 11: GROMOS96 43a2 force field (improved alkane dihedrals)
>> 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>> 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>> 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>> 16: [DEPRECATED] Encad all-atom force field, using full solvent charges
>> 17: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum 
>> charges
>> 18: [DEPRECATED] Gromacs force field (see manual)
>> 19: [DEPRECATED] Gromacs force field with hydrogens for NMR
>> I selected 14 ....
>> Q: should I pick 1 instead?
>> 5) combined protein and lipid structure files with cat protein_moved.pdb 
>> popc_solvated.pdb > merged.pdb, deleted some uneccessary lines 
>> and changed CRYST1 to that of the lipid  
>>  
>> 6) Obtained a sample.mdp file from 
>> http://wwwuser.gwdg.de/~ggroenh/membed.html called it g_membed_sample.mdp
>>  
>> 7) did grompp -f sample.mdp -c merged.pdb -p merged.top -o input.tpr and 
>> got this error
>>                          :-)  G  R  O  M  A  C  S  (-:
>>                Giant Rising Ordinary Mutants for A Clerical Setup
>>                             :-)  VERSION 4.5.3  (-:
>>         Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>>       Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>>         Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>>            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>>                 Michael Shirts, Alfons Sijbers, Peter Tieleman,
>>                Berk Hess, David van der Spoel, and Erik Lindahl.
>>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>             Copyright (c) 2001-2010, The GROMACS development team at
>>         Uppsala University & The Royal Institute of Technology, Sweden.
>>             check out http://www.gromacs.org <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  (-:
>> Option     Filename  Type         Description
>> ------------------------------------------------------------
>>   -f g_membed_sample.mdp  Input        grompp input file with MD parameters
>>  -po      mdout.mdp  Output       grompp input file with MD parameters
>>   -c     merged.pdb  Input        Structure file: gro g96 pdb tpr etc.
>>   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>>  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>>   -n      index.ndx  Input, Opt.  Index file
>>   -p     merged.top  Input        Topology file
>>  -pp  processed.top  Output, Opt. Topology file
>>   -o      input.tpr  Output       Run input file: tpr tpb tpa
>>   -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>>   -e       ener.edr  Input, Opt.  Energy file
>> Option       Type   Value   Description
>> ------------------------------------------------------
>> -[no]h       bool   no      Print help info and quit
>> -[no]version bool   no      Print version info and quit
>> -nice        int    0       Set the nicelevel
>> -[no]v       bool   no      Be loud and noisy
>> -time        real   -1      Take frame at or first after this time.
>> -[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
>>                             sites
>> -maxwarn     int    0       Number of allowed warnings during input 
>> processing
>> -[no]zero    bool   no      Set parameters for bonded interactions without
>>                             defaults to zero instead of generating an error
>> -[no]renum   bool   yes     Renumber atomtypes and minimize number of
>>                             atomtypes
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
>> NOTE 1 [file g_membed_sample.mdp]:
>>   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>>   nstcomm to nstcalcenergy
>> Generated 165 of the 1596 non-bonded parameter combinations
>> -------------------------------------------------------
>> Program grompp, VERSION 4.5.3
>> Source code file: toppush.c, line: 1166
>> Fatal error:
>> Atomtype LC3 not found
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> "Your Country Needs YOU" (U.S. Army)
>>  
>> 8) My merged.top looks like this
>>  
>> ; Include forcefield parameters
>> #include "gromos53a6.ff/forcefield.itp"
>>  
>> ;Include Protein Topology
>> #include "protein.itp"
>>  
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>> ;
>> ;
>> ;Include POPC topology
>> #include "popc.itp"
>> ;
>> ;Include water topology
>> #include "gromos53a6.ff/spc.itp"
>>  
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>    1    1       1000       1000       1000
>> #endif
>>  
>> ; Include topology for ions
>> #include "gromos53a6.ff/ions.itp"
>>  
>> [ system ]
>> ; Name
>> POPC in water + Protein
>>  
>> [ molecules ]
>> ; Compound        #mols
>> Protein_X                       1
>> POPC                339
>> SOL         16865
>> I am certain I have LC3 in the ffnonbonded.itp file I created in step 
>> (1)... 
>>  
>> Many thanks for your help in advance.
>>  
>> Huiwen
>>  
>>  
>>  
>> <<
>>
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>> Please do not use, copy or disclose the information contained in this 
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>>  >>
>> <<
>>
>> This message and any attachment are intended solely for the addressee 
>> and may contain confidential information. If you have received this 
>> message in error, please send it back to me, and immediately delete it. 
>> Please do not use, copy or disclose the information contained in this 
>> message or in any attachment. Any views or opinions expressed by the 
>> author of this email do not necessarily reflect the views of the 
>> University of Nottingham.
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>> This message has been checked for viruses but the contents of an 
>> attachment may still contain software viruses which could damage your 
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> 

-- 
========================================

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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This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>



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