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"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
[ 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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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:
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Copyright (c) 2001-2015, The GROMACS development team at
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check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
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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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