[gmx-users] simulation a box of water
Saeed Nasiri
s.t.nasiri at gmail.com
Sat Apr 2 18:59:01 CEST 2016
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
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 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
-------------------------------------------------------
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.
--------------------------------------------------------------------------
*~/Desktop/water_box $ gmx_mpi mdrun -v -deffnm nvt*
:-) GROMACS - gmx mdrun, 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 mdrun, VERSION 5.1.2
Executable: /usr/local/gromacs/bin/gmx_mpi
Data prefix: /usr/local/gromacs
Command line:
gmx_mpi mdrun -v -deffnm nvt
-------------------------------------------------------
Program: gmx mdrun, VERSION 5.1.2
Source file: src/gromacs/options/options.cpp (line 248)
Function: void gmx::Options::finish()
*Error in user input:Invalid input values In option s Required option
was not provided, and the default file 'topol' does not exist or is not
accessible. The following extensions were tried to complete the file
name: .tpr*
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Halting program gmx mdrun
--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------
#################### *NVT.mdp* #################################
title = OPLS water NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy
atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with
Verlet
rcoulomb = 1.0 ; short-range electrostatic cutoff
(in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in
nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 298.15 298.15 ; reference
temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell
distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
###########################################################################
More information about the gromacs.org_gmx-users
mailing list