From: Shaon Chakrabarti (shaonc_at_gmail.com)
Date: Mon Dec 31 2012 - 14:35:50 CST
Dear NAMD experts,
I generated some umbrella sampling data using the NPT
ensemble in NAMD. Now I'd like to use WHAM to generate
the PMF, but I've written my WHAM code using the NVT
ensemble (since all textbooks on the subject derive it using
NVT!). (Why don't I generate NVT trajectories? I did, but for some
reason which I can't figure out, the water box is getting completely
deformed in the NVT trajectories!)
Could someone please tell me if it's ok to use NVT WHAM
on NPT trajectories? If the relative volume fluctuations are very small
in the NPT simulations (my water box dimensions are 50x50x50),
then I can expect the results from NVT wham to be correct, can't I?
Or will I have to rederive the WHAM equations in NPT?
I'd be be grateful for any help regarding this matter.
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