[gmx-users] simulation a box of water

Sat Apr 2 08:39:04 CEST 2016

Hi Saeed,

Us a larger box, like edge length 2.5 or 3. The non-matching names are not
much of a problem, and you can add -maxwarn 1 to the grompp call.

Cheers,

Tsjerk
On Apr 2, 2016 8:29 AM, "Saeed Nasiri" <s.t.nasiri at gmail.com> wrote:

> thank you TsjerkI modified the topology file and did all the thing from the
> begnning, but there is another error!
>
>
>
>
>
> *gmx_mpi insert-molecules -ci WATER.pdb -nmol 500  -box 2 2 2 -o
> water_box.gro*
> ...
> ...
> ...
>
>  Try 5000
> *Added 392 molecules (out of 500 requested)*
> Writing generated configuration to water_box.gro
>
> Output configuration contains 1176 atoms in 784 residues
> ...
> ...
>
>
> *******************************************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
>
> [ system ]
> A box of water
>
> [ molecules ]
> *SOL     392*
>
> ************************************************************************************************
> ~/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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> Bjelkmar
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>   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
>
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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
> 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 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
>
>
> 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 26722793
> 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
> Excluding 2 bonded neighbours molecule type 'SOL'
> Warning: atom name 1 in topol.top and water_box.gro does not match (OW - O)
> Warning: atom name 2 in topol.top and water_box.gro does not match (HW1 -
> H)
> Warning: atom name 3 in topol.top and water_box.gro does not match (HW2 -
> H)
> Warning: atom name 4 in topol.top and water_box.gro does not match (OW - O)
> Warning: atom name 5 in topol.top and water_box.gro does not match (HW1 -
> H)
> Warning: atom name 6 in topol.top and water_box.gro does not match (HW2 -
> H)
> Warning: atom name 7 in topol.top and water_box.gro does not match (OW - O)
> Warning: atom name 8 in topol.top and water_box.gro does not match (HW1 -
> H)
> Warning: atom name 9 in topol.top and water_box.gro does not match (HW2 -
> H)
> Warning: atom name 10 in topol.top and water_box.gro does not match (OW -
> O)
> Warning: atom name 11 in topol.top and water_box.gro does not match (HW1 -
> H)
> Warning: atom name 12 in topol.top and water_box.gro does not match (HW2 -
> H)
> Warning: atom name 13 in topol.top and water_box.gro does not match (OW -
> O)
> Warning: atom name 14 in topol.top and water_box.gro does not match (HW1 -
> H)
> Warning: atom name 15 in topol.top and water_box.gro does not match (HW2 -
> H)
> Warning: atom name 16 in topol.top and water_box.gro does not match (OW -
> O)
> Warning: atom name 17 in topol.top and water_box.gro does not match (HW1 -
> H)
> Warning: atom name 18 in topol.top and water_box.gro does not match (HW2 -
> H)
> Warning: atom name 19 in topol.top and water_box.gro does not match (OW -
> O)
> Warning: atom name 20 in topol.top and water_box.gro does not match (HW1 -
> H)
> (more than 20 non-matching atom names)
>
>
>
>
> *WARNING 1 [file topol.top, line 19]:  1176 non-matching atom names  atom
> names from topol.top will be used  atom names from water_box.gro will be
> ignored*
>
>
>
>
>
>
> *ERROR 1 [file topol.top, line 19]:  ERROR: The cut-off length is longer
> than half the shortest box vector or  longer than the smallest box diagonal
> element. Increase the box size or  decrease rlist.*
>
>
> Removing all charge groups because cutoff-scheme=Verlet
>
>
>
> *There was 1 noteThere was 1 warning*
>
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1.2
> Source code file:
> /home/nasiri/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 1738
>
>
> *Fatal error:There was 1 error in input file(s)*
> 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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