Fw: Fw: [gmx-users] How to restart the crashed run

[Mahboobeh Eslami]

dear mark 

thank you so much
Good luck

----- Forwarded Message -----
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 1:21 PM
Subject: Re: Fw: [gmx-users] How to restart the crashed run
 

mdrun -v -deffnm md -cpi md

IIRC the -cpi file is immune from -deffnm

Mark

On Tue, Sep 17, 2013 at 4:48 AM, Mahboobeh Eslami
<mahboobeh.eslami at yahoo.com> wrote:
> dear mark
>
> yes i do
> my comment for md run was following
>
>
> mdrun -v -deffnm md >& md.job &
>
> now what comment is true for restart?
> I've recently started working with the gromacs and i am not professional
>  thank you and best wishes for you
>
> ----- Forwarded Message -----
> 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 12:23 PM
> Subject: Re: [gmx-users] How to restart the crashed run
>
>
> 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
>>>>
>>>> --
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