[gmx-users] simulation a box of water

Saeed Nasiri s.t.nasiri at gmail.com
Sat Apr 2 08:05:46 CEST 2016

Dear users

I have constructed a box of only water molecules, but I don't know how to
constructed the topology file. I wrote this file but it didn't work.

Some commentary will be very appreciated.
Thank you for advance.

************************************* topol.top *
#include "oplsaa.ff/forcefield.itp"
; Include water topology
#include "oplsaa.ff/tip3p.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

[ molecules ]
SOL     1690
*~/Desktop/water_box $  gmx_mpi grompp -f minim.mdp -c water_box.gro -o
em.tpr -p topol.top *
                  :-) GROMACS - gmx grompp, VERSION 5.1.2 (-:

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GROMACS:      gmx grompp, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx_mpi
Data prefix:  /usr/local/gromacs
Command line:
  gmx_mpi grompp -f minim.mdp -c water_box.gro -o em.tpr -p topol.top

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#

NOTE 1 [file minim.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 2889297176
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations

Program gmx grompp, VERSION 5.1.2
Source code file:
/home/nasiri/gromacs-5.1.2/src/gromacs/gmxpreprocess/topio.c, line: 755

*Fatal error:Syntax error - File topol.top, line 15Last line read:'[
molecules ]'Invalid order for directive molecules*
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Halting program gmx grompp
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.

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