[gmx-users] problem to restart REMD

[leila salimi]

I understand what you meant, I run only few steps for the other replicas
and then continue with the whole replicas.
I hope every thing is going well.

Thanks very much.

On Wed, Jun 17, 2015 at 11:43 PM, leila salimi <leilasalimi at gmail.com>
wrote:

> Thanks Mark for your suggestion.
> Actually I don't understand the new two state6.cpt and state7,cpt files,
> because the time that it shows is  127670.062  !
> That is strange! because my time step is 2 fs and I saved the output every
> 250 steps, means every 500 fs. I expect the time should be like 127670.000
> or 127670.500 .
>
> By the way you mean with mdrun_mpi ... -nsteps ... , I can get the steps
> that I need for the old state.cpt files?
>
> Regards,
> Leila
>
> On Wed, Jun 17, 2015 at 11:22 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> That's all extremely strange. Given that you aren't going to exchange in
>> that short period of time, you can probably do some arithmetic and work
>> out
>> how many steps you'd need to advance whichever set of files is behind the
>> other. Then mdrun_mpi ... -nsteps y can write a set of checkpoint files
>> that will be all at the same time!
>>
>> Mark
>>
>> On Wed, Jun 17, 2015 at 10:18 PM leila salimi <leilasalimi at gmail.com>
>> wrote:
>>
>> > Hi Mark,
>> >
>> > Thanks very much. Unfortunately both the state6.cpt, state6_prev,cpt and
>> > state7.cpt and state7_prev.cpt updated and their time are different from
>> > other replicas file (also with *_prev.cpt )!
>> >
>> > I am thinking maybe I can use init-step in mdp file, and start from the
>> > time that I have, because all trr files have the same time! I checked
>> with
>> > gmxcheck. But I am not sure that I will get correct results!
>> > Actually I got confused that with the mentioned Note, only two replicas
>> > were running and the state file is changed and the others not!
>> >
>> > ​regards,
>> > Leila
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