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

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 9 18:52:01 CEST 2018


Probably your initial working directory is not what you expect it to be.
That's often supposed to be set in your job script. Check out the
documentation for your cluster or submission system, and then ask the


On Mon, Apr 9, 2018, 17:25 neelam wafa <neelam.wafa at gmail.com> 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.
> Thanks in advance.
> Regards
> Neelam wafa
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