Great. I gave it a go and the MMPBSA calculation is performed over 480 frames.
When I run it through ptraj - i get out 505 frames.
This seems to be the 480 frames + 1 extra frame per CPU core (24) + 1 extra.
Is there some overlap between the files, or do I need to specify the input to ptraj in a particular way.
Thanks,
Jesper
Den 29/08/2011 kl. 16.22 skrev Bill Miller III:
> Yes, that should be correct.
>
> -Bill
>
> 2011/8/29 Jesper Sørensen <lists.jsx.dk>
>
>> Hi,
>>
>> When I run MMPBSA.py in parallel it splits up the file for each CPU-core,
>> to something like this below.
>>
>> 2.4M _MMPBSA_mutant_receptor.mdcrd.0
>> 2.3M _MMPBSA_mutant_receptor.mdcrd.1
>> 2.3M _MMPBSA_mutant_receptor.mdcrd.2
>> 2.3M _MMPBSA_mutant_receptor.mdcrd.3
>> 2.3M _MMPBSA_mutant_receptor.mdcrd.4
>> 2.3M _MMPBSA_mutant_receptor.mdcrd.5
>> 2.3M _MMPBSA_mutant_receptor.mdcrd.6
>> 2.3M _MMPBSA_mutant_receptor.mdcrd.7
>>
>> If I wanted to cat these together using ptraj, is the ordering of the files
>> so that I can just cat 0, 1, 2, 3 etc. and the frames will be in the
>> correct order as in the initial MD trajectory?
>>
>> Best regards,
>> Jesper
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>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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Received on Mon Aug 29 2011 - 17:00:02 PDT
