[gmx-users] How to restart the crashed run

[Mark Abraham]

You named them last time you ran mdrun, either explicitly or with
-deffnm. Do the same.

Mark

On Tue, Sep 17, 2013 at 3:19 AM, Mahboobeh Eslami
<mahboobeh.eslami at yahoo.com> wrote:
> when i use following  omment for restart
>
> mdrun -s md.tpr -cpi md.cpt
> i get following error
>
> Output file appending has been requested,
> but some output files listed in the checkpoint file md.cpt
> are not present or are named differently by the current program:
> output files present: md.log
> output files not present or named differently: md.trr md.edr
>
>
> but i have md.trr  and md.edr in my folder.
>
> thank you so much
>
>
> ----- Forwarded Message -----
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Tuesday, September 17, 2013 11:22 AM
> Subject: Re: [gmx-users] How to restart the crashed run
>
>
> Hi,
>
> 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 :-)
>
> Mark
>
>
> 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
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists