On Mon, Oct 3, 2011 at 2:01 PM, George Tzotzos <gtzotzos.me.com> wrote:
> 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.
>
Normal mode estimates are fairly unreliable. As expensive as the Hessian
construction/diagonalization is (we're helped by the fact that it's an
analytical Hessian, I think), in my experience the minimization takes
significantly longer. However, the number of steps required to minimize
within tolerable limits obviously depends on how close the structure is to a
minimum initially. MMPBSA.MPI's parallelization scheme is naive, though,
and assumes each will take the same amount of time, which hurts parallel
scaling for normal mode calcs in most cases.
>
> My question is whether increasing nminterval to 100 would compensate the
> accuracy of the calculation.
>
Unlikely (though maybe increase it to 50 instead). Keep in mind that NMODE
frames are minimized, so in all likelihood many of your snapshots are very
structurally similar to others (if they reduce to the same local minimum).
A better approach may be to perform normal mode analysis on clustered
trajectories, and only take one snapshot from each cluster (or something
like that). You can always check existing literature to see what they've
done as well.
HTH,
Jason
> Thanks in advance
>
> George
>
>
>
>
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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 Oct 03 2011 - 13:00:04 PDT
