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

[Sun Iba]

The single code from script reproduced the same error:

C































*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 5.0Executable:
/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. gmx grompp and dint use the
script and the command worked smoothly. The first minimization step is
complete. I dont know why there is "File input/output" error with script. 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 with the job.sh?*

On Sat, Sep 3, 2016 at 10:00 AM, sun.iba2 <sun.iba2 at gmail.com> wrote:

> Yes. Doing that. Thank you very much.
>
>
> Sent from Samsung Mobile
>
>
> -------- Original message --------
> From: Nikhil Maroli <scinikhil at gmail.com>
> Date:02/09/2016 7:28 PM (GMT+05:30)
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Cc:
> Subject: Re: [gmx-users] Free energy calculation, Methane in water
> tutorial
>
> run the single code from script and see what prints on the screen,that's
> what Justin suggested
> --
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