I did add the 0th trajectory file and yes that is where the "+1 extra comes from", but I am still getting 1 extra frame per file/CPU-core, so in total 24 extra frames in the ptraj combined mdcrd file.
I am preparing files for double-ala mutations, based on the single-ala mutations I have already performed.
Best,
Jesper
Den 29/08/2011 kl. 19.32 skrev Jason Swails:
> 2011/8/29 Jesper Sørensen <lists.jsx.dk>
>
>> 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.
>>
>
> There should be no overlap between the files, and you should be able to add
> up each file in numerical order to build the original trajectory. I'm
> confused about what exactly you're doing here... Did you remember to trajin
> the 0th trajectory? Based on the sizes you gave above, I would expect the
> 0th trajectory to have 1 more frame than each other (since the total number
> of frames mod the number of processors was 1), so it seems that you didn't
> run the 0th frame through MMPBSA, which will account for what you are
> seeing...
>
> HTH,
> Jason
>
>
>> 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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>>
>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Aug 29 2011 - 20:00:03 PDT
