[gmx-users] simulation a box of water

Saeed Nasiri s.t.nasiri at gmail.com
Wed Mar 16 13:31:01 CET 2016

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:

*gmx_mpi insert-molecules -ci WATER.pdb -nmol 3000 -box 2 2 2 -o
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"

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
 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
    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:
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

Using the Oplsaa force field in directory oplsaa.ff

Opening force field file

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
 5: TIP5P  TIP 5-point improved for Ewald sums
 6: SPC    simple point charge
 7: SPC/E  extended simple point charge
 8: None
Opening force field file
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
Atomtype 814
Reading residue database... (oplsaa)
Opening force field file
Residue 52
Sorting it all out...
Opening force field file
Opening force field file
Opening force field file

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?

More information about the gromacs.org_gmx-users mailing list