Thanks sir Mark and Justin.
I ll try to figure it out with the administer. But  in case the problem is
not resolved, is it okay if I run the commands directly through terminal?
Will it effect the results?
I know it ll be a tedious job.

Regards
Neelam Wafa

On Mon, 9 Apr 2018 10:03 pm Justin Lemkul, <jalem...@vt.edu> wrote:

>
>
> On 4/9/18 12:56 PM, neelam wafa wrote:
> > Thanks Sir for your quick response.
> > These are the errors I am getting.
> > Error in user input:
> > Invalid command-line options
> >    In command-line option -f
> >      File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not
> exist
> > or
> >      is not accessible.
> >    In command-line option -c
> >      File '/home/Downloads/Free_Energy/Methane/methane_water.gro' does
> not
> >      exist or is not accessible.
> >    In command-line option -p
> >      File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist
> or
> > is
> >      not accessible.
> > job.sh: line 30: mdrun: command not found
> >
> >
> > Error in user input:
> > Invalid command-line options
> >    In command-line option -f
> >      File '/home/Downloads/Free_Energy/MDP/NVT/nvt_0.mdp' does not exist
> or
> > is
> >      not accessible.
> >    In command-line option -p
> >      File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist
> or
> > is
> >      not accessible.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > job.sh: line 65: mdrun: command not found
> >
> > similar errors I get for all the sets.
>
> It seems that the compute node has no idea where your files or
> executables are, which means however you've configured your job script
> is incorrect for your cluster. Consult your system administrator, as
> none of these problems are actually specific to GROMACS.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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