I'm running MMPBSA.MPI on 12 processors. I'm trying to compute the entropy (nmode) of a protein/ligand complex from a 10ns trajectory (1000) frames.
My entropy.in is:
Input file for running entropy calculations using NMode
&general
endframe=1000, keep_files=2,
/
&nmode
nmstartframe=10, nmendframe=990,
nminterval=10, nmode_igb=1, nmode_istrng=0.1,
/
My estimate is that it'll take at least 10 hours to get results.
My question is whether increasing nminterval to 100 would compensate the accuracy of the calculation.
Thanks in advance
George
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Received on Mon Oct 03 2011 - 11:30:03 PDT
