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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