[gmx-users] simulation a box of water

Pradip Kaur kaur.pradip253 at gmail.com
Wed Mar 16 16:32:21 CET 2016 

you have to select water molecule for running the simulation .choose water
model SPC nd then run the command. I hope then it will work

On 16 March 2016 at 18:51, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/16/16 8:30 AM, Saeed Nasiri wrote:
>
>> Dear all
>>
>> I want to simulate a box of water (2*2*2 nm with 1401 molecules). Is there
>> difference between using a model for water molecules and importing this
>> molecule from other programs(such as nwchem)?
>> I want to do a small simulation and it is not important to treat water
>> molecules explicitly.
>> I used a water.pdb file to generate the box with this command:
>>
>>
> I'm confused.  You don't need to treat water explicitly, but you're
> building a box of explicit water molecules?  Can you please explain in
> greater detail what you're trying to accomplish?  If you have a custom set
> of water parameters, you need to introduce these yourself in suitable
> GROMACS format.
>
> pdb2gmx generates topologies.  By executing it in the manner below, you
> are essentially telling pdb2gmx "I have water, but don't write a topology
> for water" so pdb2gmx correctly fails.
>
> -Justin
>
>
>
>> *gmx_mpi insert-molecules -ci WATER.pdb -nmol 3000 -box 2 2 2 -o
>> water_box.gro*
>>   ...
>>   ....
>> Added 467 molecules (out of 3000 requested)
>> Writing generated configuration to water_box.gro
>>
>> Output configuration contains 1401 atoms in 934 residues
>>
>> gcq#247: "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix"
>> (Indeep)
>>
>> after that I want to create topol.gro file, but I got an error ?
>>
>>
>> *gmx_mpi pdb2gmx -f water_box.gro -o water_box2.gro -ignh*
>>                    :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:
>>
>>                              GROMACS is written by:
>>       Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
>> Bjelkmar
>>   Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian
>> Fritsch
>>    Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent
>> Hindriksen
>>   Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten
>> Kutzner
>>      Per Larsson      Justin A. Lemkul   Magnus Lundborg   Pieter
>> Meulenhoff
>>     Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk
>>     Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons
>> Sijbers
>>     Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf
>>                             and the project leaders:
>>          Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2015, The GROMACS development team at
>> Uppsala University, Stockholm University and
>> the Royal Institute of Technology, Sweden.
>> check out http://www.gromacs.org for more information.
>>
>> GROMACS is free software; you can redistribute it and/or modify it
>> under the terms of the GNU Lesser General Public License
>> as published by the Free Software Foundation; either version 2.1
>> of the License, or (at your option) any later version.
>>
>> GROMACS:      gmx pdb2gmx, VERSION 5.1.2
>> Executable:   /usr/local/gromacs/bin/gmx_mpi
>> Data prefix:  /usr/local/gromacs
>> Command line:
>>    gmx_mpi pdb2gmx -f water_box.gro -o water_box2.gro -ignh
>>
>>
>> Select the Force Field:
>>  From '/usr/local/gromacs/share/gromacs/top':
>>   1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
>> 1999-2012, 2003)
>>   2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>>   3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
>> 461-469, 1996)
>>   4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
>> 1049-1074, 2000)
>>   5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
>> 712-725, 2006)
>>   6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
>> Proteins 78, 1950-58, 2010)
>>   7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>>   8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
>>   9: GROMOS96 43a1 force field
>> 10: GROMOS96 43a2 force field (improved alkane dihedrals)
>> 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>> 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>> 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>> 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
>> 10.1007/s00249-011-0700-9)
>> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>> 15
>>
>> Using the Oplsaa force field in directory oplsaa.ff
>>
>> Opening force field file
>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermodels.dat
>>
>> Select the Water Model:
>>   1: TIP4P  TIP 4-point, recommended
>>   2: TIP4PEW TIP 4-point with Ewald
>>   3: TIP3P  TIP 3-point
>>   4: TIP5P  TIP 5-point (see http://redmine.gromacs.org/issues/1348 for
>> issues)
>>   5: TIP5P  TIP 5-point improved for Ewald sums
>>   6: SPC    simple point charge
>>   7: SPC/E  extended simple point charge
>>   8: None
>> 8
>> Opening force field file
>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
>> Reading water_box.gro...
>> Read 'UNNAMED', 467 atoms
>> Analyzing pdb file
>> Splitting chemical chains based on TER records or chain id changing.
>> There are 0 chains and 1 blocks of water and 934 residues with 467 atoms
>>
>>    chain  #res #atoms
>>    1 ' '   933    467  (only water)
>>
>> No occupancies in water_box.gro
>> Opening force field file
>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
>> Atomtype 814
>> Reading residue database... (oplsaa)
>> Opening force field file
>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
>> Residue 52
>> Sorting it all out...
>> Opening force field file
>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
>> Opening force field file
>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
>> Opening force field file
>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
>>
>> Back Off! I just backed up topol.top to ./#topol.top.1#
>> Processing chain 1 (467 atoms, 933 residues)
>> Problem with chain definition, or missing terminal residues.
>> This chain does not appear to contain a recognized chain molecule.
>> If this is incorrect, you can edit residuetypes.dat to modify the
>> behavior.
>> 8 out of 8 lines of specbond.dat converted successfully
>> Checking for duplicate atoms....
>> Generating any missing hydrogen atoms and/or adding termini.
>> Now there are 933 residues with 1401 atoms
>> Making bonds...
>> Number of bonds was 1866, now 934
>> Generating angles, dihedrals and pairs...
>> Making cmap torsions...
>> There are    0 dihedrals,    0 impropers,  467 angles
>>               0 pairs,      934 bonds and     0 virtual sites
>> Total mass 8413.192 a.m.u.
>> Total charge 0.000 e
>>
>> -------------------------------------------------------
>> Program gmx pdb2gmx, VERSION 5.1.2
>> Source code file:
>> /home/nasiri/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 2159
>>
>>
>> *Fatal error:You have chosen not to include a water model, but there is
>> water in the input file. Select a water model or remove the water from
>> your
>> input file.*
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> Halting program gmx pdb2gmx
>> --------------------------------------------------------------------------
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 1.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>>
>>
>> I would be appreciate if anyone could  help me?
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
> --
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