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 (-:
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.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
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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