[gmx-users] Help calculation on cluster

[Smith, Micholas D.]

Try:

echo "0" | g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -nodecomp -apol apolar.xvg -nodiff

In your submission file. Where "0" is the index number of the group you are interested in.

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mishelle Oña <samimishu at hotmail.com>
Sent: Friday, December 18, 2015 3:04 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Help calculation on cluster

Thanks for your reply Micholas, I ask my system admins but he told me that for queuing the job I need to enter the selected group in the command line. My command is g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -nodecomp -apol apolar.xvg -nodiff
My question was if I can add something to this command in order to select the atom group I  wanted to use instead of selecting it from the group list that appears after the job is submitted?
Mishelle

> From: smithmd at ornl.gov
> To: gmx-users at gromacs.org
> Date: Fri, 18 Dec 2015 19:47:22 +0000
> Subject: Re: [gmx-users] Help calculation on cluster
>
> Not really the best place to ask this question (check with your system admins), but....
>
> You could run your command from a "screen session".
>
> Just run screen when you first log into the machine, go about your business setting up your simulation and then start it. Once it is running, type control-a-d to detach from the session. It will continue to run until completion, or the computer crashes, whether you close the terminal or not. And you can always re-attach to the screen session to see what is going on from a new terminal if you need to.
>
> Ideally, though, you would just submit your job to a queuing system and wait for it to finish...be sure to check with your sys. admins.
>
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mishelle Oña <samimishu at hotmail.com>
> Sent: Friday, December 18, 2015 2:40 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Help calculation on cluster
>
> Hi,
> I am doing some simulations in a cluster. I want to know if there is an option to run the simulation in order that I can close the terminal?. I tried to make  sbatch but the problem is that when I entered the command there is a step to choose the system and with sbatch I could not choose this option.
> Thank youMishelle
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