[gmx-users] Free energy calculation, Methane in water tutorial

[Sun Iba]

The single code from script reproduced the same error:

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*ommand line:  gmx grompp -f /home/Documents/tutorial/MDP/EM/em_steep.mdp
-c /home/Documents/tutorial/Methane/methane_water.gro -p
/home/Documents/tutorial/Methane/topol.top -o
min.tpr-------------------------------------------------------Program gmx,
VERSION 5.0Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/futil.cpp, line:
540File input/output error:/home/Documents/tutorial/MDP/EM/em_steep.mdpFor
more information and tips for troubleshooting, please check the
GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
<http://www.gromacs.org/Documentation/Errors>-------------------------------------------------------GROMACS:
gmx mdrun, VERSION 5.0GROMACS 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 Peter Kasson       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
Christian Wennberg Maarten Wolf       and the project leaders:Mark Abraham,
Berk Hess, Erik Lindahl, and David van der SpoelCopyright (c) 1991-2000,
University of Groningen, The Netherlands.Copyright (c) 2001-2014, The
GROMACS development team atUppsala University, Stockholm University andthe
Royal Institute of Technology, Sweden.check out http://www.gromacs.org
<http://www.gromacs.org> for more information.GROMACS is free software; you
can redistribute it and/or modify itunder the terms of the GNU Lesser
General Public Licenseas published by the Free Software Foundation; either
version 2.1of the License, or (at your option) any later
version.GROMACS:      gmx mdrun, VERSION 5.0Executable:
/usr/local/gromacs/bin/gmxLibrary dir:
/usr/local/gromacs/share/gromacs/topCommand line:  mdrun -nt 2 -deffnm
min0Back Off! I just backed up min0.log to
./#min0.log.5#-------------------------------------------------------Program
mdrun, VERSION 5.0Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line:
513Can not open file:min0.tprFor more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentati <http://www.gromacs.org/Documentati>*
on/Errors
-------------------------------------------------------


However, I tried using normal command i.e. I dint use the script and the
command worked smoothly. The minimization step is complete. I dont know why
there is "File input/output" error. I have placed the .mdp files in
/home/Docuemnts/tutorial/MDP/EM, as I mentioned in .sh file:


#!/bin/bash

# Set some environment variables
FREE_ENERGY=/home/Documents/tutorial
echo "Free energy home directory set to $FREE_ENERGY"

MDP=$FREE_ENERGY/MDP/EM
echo ".mdp files are stored in $MDP"

LAMBDA=0

# A new directory will be created for each value of lambda and
# at each step in the workflow for maximum organization.

mkdir Lambda_$LAMBDA
cd Lambda_$LAMBDA

#################################
# ENERGY MINIMIZATION 1: STEEP  #
#################################
echo "Starting minimization for lambda = $LAMBDA..."

mkdir EM_1
cd EM_1

# Iterative calls to grompp and mdrun to run the simulations

gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c
$FREE_ENERGY/Methane/methane_water.gro -p $FREE_ENERGY/Methane/topol.top -o
min$LAMBDA.tpr

mdrun -nt 2 -deffnm min$LAMBDA

sleep 10


Have I messed up the job.sh?

On Fri, Sep 2, 2016 at 7:28 PM, Nikhil Maroli <scinikhil at gmail.com> wrote:

> run the single code from script and see what prints on the screen,that's
> what Justin suggested
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