[gmx-users] How to extend correctly pulling simulation?

Berk Hess gmx3 at hotmail.com
Mon Jun 22 16:44:58 CEST 2009


You don't say why you want to do it in several simulations and not in one.
If it is just because your runtime per job is limited you can use
the standard way to cut any simulation into parts.
Make a tpr file with nsteps set to all steps.
run it with mdrun -cpi -append -maxh <hours>
Then mdrun will append the output of the new parts to the old parts.


> Date: Mon, 22 Jun 2009 15:20:16 +0200
> From: mhviet at ifpan.edu.pl
> To: gmx-users at gromacs.org
> Subject: [gmx-users] How to extend correctly pulling simulation?
> Hi all,
>   I am trying to stretch protein using gromacs 4.0 umbrella options.
> (please see mdp file in attachment).
>  This is quite large 136 amino acids protein which I want to stretch
> completely using sets of mdp files with 250000 numbers of steps.  To
> perform these simulations I have to be able to continue my MD simulation
> after each successful run. Could you give me advice which options I
> should add or change to perform these simulations in a correct way.
> Thanks a lot in advance
> Maksim Kouza
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