[gmx-users] simulation a box of water

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
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 (-:

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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?