[gmx-users] simulation a box of water

Justin Lemkul jalemkul at vt.edu
Wed Mar 16 14:21:31 CET 2016 


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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