[AMBER] How to do QHA with outputs after considering every n-frames of trajectory?

From: SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
Date: Tue, 24 May 2016 23:46:56 +0530


I am trying to estimate entropic contribution to the binding free energy
for binding of a small drug-like molecule to 286 residue receptor using QHA
with MMPBSA.py. I am using AmberTools15. My simulation run is 1
micro-second, frames saved every 1ps, and I am able to get entropy
estimates from entire 1 micro-sec, but I am interested in convergence of
these estimates as well, are there any ways to output QHA values say after
(100, 200, 300, 400 .. 900ns) so that convergence can be checked.

My problem is that running this analysis takes me ~20 days on 48-core
SMP-machine for 1 micro-second simulation. this way being able to run in
above mentioned way seems unfeasible.

Any suggestion in this regard would be very helpful.

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Received on Tue May 24 2016 - 11:30:02 PDT
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