[gmx-users] How to restart the crashed run

Mark Abraham mark.j.abraham at gmail.com
Tue Sep 17 08:52:32 CEST 2013


Please keep discussion on the mailing list.

If you have a .cpt file that is not called state.cpt, then you must
have asked for the checkpoint file to be named md.cpt in your original
mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the
default filename (and mostly there is no reason to change that).
Simply use md.cpt, now that you have it :-)


On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami
<mahboobeh.eslami at yahoo.com> wrote:
> I have md.cpt but I don't have restart my run
> What is the purpose of the state.cpt file?
> thank you so much
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Mahboobeh Eslami <mahboobeh.eslami at yahoo.com>; Discussion list for
> GROMACS users <gmx-users at gromacs.org>
> Sent: Tuesday, September 17, 2013 9:36 AM
> Subject: Re: [gmx-users] How to restart the crashed run
> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests
> the 3.x-era restart strategy when checkpoint files are unavailable.
> But if you simply have no output files, then you have no ability to
> restart.
> Mark
> On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami
> <mahboobeh.eslami at yahoo.com> wrote:
>> hi my friends
>> please help me
>> i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near
>> the end of the simulation
>> How to restart the crashed run?
>>  in the gromacs.org following comment has been proposed
>> mdrun -s topol.tpr -cpi state.cpt
>> but i don't have state.cpt in my folder.
>> I need urgent help
>> Thank you very much
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