On 4/2/16 12:58 PM, Saeed Nasiri wrote:
Dear users
I used the "define= -DFLEXIBL" option and the problem within the energy
minimization step has been solved. However, there is another problem in the
nvt equilibration step. please help me with this problem!
Thanks in advanced.
* ~/Desktop/water_box $ gmx_mpi grompp -f nvt.mdp -c em.gro -p topol.top -o
nvt.tpr -maxwarn 1*
:-) GROMACS - gmx grompp, VERSION 5.1.2 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
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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:
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
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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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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 nvt.mdp -c em.gro -p topol.top -o nvt.tpr -maxwarn 1
Ignoring obsolete mdp entry 'title'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
Setting the LD random seed to 3338597373
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'
turning all bonds into constraints...
Setting gen_seed to 3746256358
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 1000 Water residues
-------------------------------------------------------
Program gmx grompp, VERSION 5.1.2
Source code file:
/home/nasiri/gromacs-5.1.2/src/gromacs/gmxpreprocess/readir.c, line: 2585
*Fatal error:Group Protein referenced in the .mdp file was not found in the
index file.Group names must match either [moleculetype] names or custom
index groupnames, in which case you must supply an index file to the '-n'
optionof grompp.*
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
It's right here:
tc-grps = Protein Non-Protein ; two coupling groups - more
If you have only a box of water, you don't have protein...
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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