[gmx-users] simulation a box of water

[Tsjerk Wassenaar]

Hi Saeed,

Just before [ molecules ] insert the lines:

[ system ]
A box of water

Cheers,

Tsjerk
On Apr 2, 2016 8:06 AM, "Saeed Nasiri" <s.t.nasiri at gmail.com> wrote:

> 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 (-:
>
>                             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.
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> check out http://www.gromacs.org for more information.
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> GROMACS is free software; you can redistribute it and/or modify it
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> as published by the Free Software Foundation; either version 2.1
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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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