Thanks Jason for reply.
But if I take average of two will it be mathematicaly correct? Because I am
calculating initial 100ps of 200ps trajectory and next 100ps of same separately.
So how I can claculate entropy of 200ps by taking average of two 100ps trajectory.
I am bit confused here.
> If they're both the same number of frames, you could just average the two of
> them (otherwise you'd obviously have to weight one more than the other).
>
> If you have all of the temporary _MMPBSA_*.mdout files from each one, you
> could concatenate each _MMPBSA_*.mdout file from one calculation onto the
> other and rerun MMPBSA.py using the flag -rewrite-outputs to have it parse
> each output file for every energy term.
>
> If you're at all uncomfortable with the second method (or you've gotten rid
> of one set of your temporary files), then use the first.
>
> HTH,
> Jason
>
> On Mon, May 9, 2011 at 7:42 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>> Hello All
>>
>> I am doing MMPBSA NMODE calculation.Earlier I have mailed regarding it,
>> since it
>> is high memory intesive process.
>> I asked whether I can divide the full trajectory of 1ns into two half or
>> not,so
>> that I can calulate it without termination of programm.
>>
>> Jason has replyed that I can break it into two and do calculation,one half
>> at a
>> time.
>>
>> First I ran nmode calculation for 200ps trajectroy then I divide it into
>> two
>> 100ps and did nmode calculation for these two 100ps trajectory.
>>
>> But I got the approx same result for 200ps and both 100ps.
>>
>> How here I can combine result of these two 100ps nmode result so that it
>> become
>> for total 200ps trajectory?
>>
>> Here I am attaching following output file:-
>>
>> 1)Output file for 200ps
>> 2)for first 100ps
>> 3)for second 100ps
>>
>>
>>
>> With regard
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Mon May 09 2011 - 21:00:03 PDT
