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, <[email protected]> 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 > > [email protected] | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
