[gmx-users] continue simulation from intermediate frame instead of last frame

[Peter Kroon]

Hi MY,


actually you lose continuity of your simulation in both cases. The cpt
file stores full precision coordinates and velocities (unlike gro/xtc).
In addition, it stores state information about the simulation itself,
such as the themostat and barostat. Whether this is an issue is up to
you of course ;)


Peter


On 04-10-17 16:24, Myunggi Yi wrote:
> 1. In principle, MD can be restarted if there are coordinates and
> velocities on the snapshot.
>
> 2. Even if you don't have velocity, you can assign random velocity with the
> specific temperature.
> In this case, you lose continuity of simulation. Don't worry.
> If you run same simulation with the exactly same inputs (including the same
> random seed), you won't get exactly same trajectory in most cases
> (depending on simulation types and hardware, etc).
>
> MY
>
>
> On Wed, Oct 4, 2017 at 9:16 AM, tarak karmakar <tarak20489 at gmail.com> wrote:
>
>> In that case, I think I do not have any option. The gmx_mpi_d check has
>> only the last frame. :(
>>
>> Command line:
>>   gmx_mpi_d check -f ../state.cpt
>>
>> Checking file ../state.cpt
>>
>> # Atoms  10703
>> Last frame         -1 time 190772.080
>>
>>
>> Item        #frames Timestep (ps)
>> Step             1
>> Time             1
>> Lambda           1
>> Coords           1
>> Velocities       1
>> Forces           0
>> Box              1
>>
>> Thanks for your replies. I appreciate it.
>>
>>
>> On Wed, Oct 4, 2017 at 3:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>> On 10/4/17 9:06 AM, tarak karmakar wrote:
>>>
>>>> Hi Justin,
>>>> Thanks for the quick reply.
>>>>
>>>> Is there any way to check if the frame is there in .cpt file or not?
>>>>
>>>> I did the following exercise at difference 'time=' values,
>>>> gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time
>>>> 40000 -o topol.tpr
>>>>
>>>> It seems in all the cases, the trajectory gets restarted from the last
>>>> frame.
>>>>
>>>>
>>> The .cpt files are always overwritten unless you tell mdrun to keep them.
>>> You can inspect the contents of any given .cpt file with gmx check.
>>>
>>> -Justin
>>>
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
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>>> Blacksburg, VA 24061
>>>
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>>>
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>>
>>
>> --
>> Regards,
>> Tarak
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