Re: A script for performing calculations divided by quanta

From: Mikhail Suyetin (msuyetin_at_gmail.com)
Date: Mon Aug 03 2009 - 10:30:28 CDT

Dear Josh, everybody,
 I need to perform a long simulation, but I cannot use my cluster all
the time. Therefore, If I want to make a simulation for a day I'll
have to split time of calculation. For example:
./run_mvapich.sh <number_of_processors> my_folder/1.namd <max_time>
<quantum_time>

--
Sincerely yours
Mikhail Suyetin
2009/8/3 Joshua Adelman <jadelman_at_berkeley.edu>:
> I'm not sure exactly what you are asking. If you want to take a long
> simulation you have run and divide the resulting trajectory into smaller
> pieces, you should use catdcd and use the '-first' and '-last' flags. On the
> other hand, if you want to run a simulation for some length of time, L, but
> want to run it in N pieces, then you would just run a number of simulations
> of length L/N and restart the n+1 simulation with the coordinates and
> velocities from simulation n. Or do you want to do something else? If so,
> you'll have to elaborate.
>
> Hope that helps.
>
> Josh
>
>
> On Aug 3, 2009, at 6:26 AM, Mikhail Suyetin wrote:
>
>> Hi everybody!
>> Does anybody have a script for performing calculations divided by
>> quanta, i.e. I would like to divide total time of MD simulation into
>> several parts.
>> --
>> Sincerely yours,
>> Mikhail Suyetin
>>
>
>

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