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

[Justin Lemkul]

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

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