[gmx-users] problem in running job.sh for free energy calculations.

[Justin Lemkul]

On 4/9/18 11:25 AM, neelam wafa wrote:
> Dear sir Justin
>
> I am doing your tutorial of free energy calculations for methane in water.
> I have created the .mdp  and  .sh files using the perl script you provided.
> I have also made the FREE_ENERGY and MDP directories as in the job. sh
> script. gro file and topology files are also in the relevant folder but
> when I run job.sh script with command bash job.sh, it says the files the
> .mdp file, the methane_water.gro file and topol.top file either dont exist
> or not accessible. I have checked the files are in their proper places and
> are searched on terminal and opened though comand with vi editor. I have
> also given chmod 777 permission to these files. but no way out of the
> problem. please help me out. I have been searching the archive and google
> for the last three days but could not sort out. When i run the grompp and
> gmx md run commands directly through the terminal it works but not through
> the job.sh.
> Please suggest me a solution. Sorry for the long text or for addressing
> directly to you.

Without specific error messages, I have nothing to go on to suggest a 
solution. Perhaps you should be consulting your system administrator if 
the commands are syntactically valid but not operational in the queued 
environment.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================