AMBER Archive (2006)

Subject: AMBER: Gibbs PMF Calculation

From: Atsutoshi Okabe (
Date: Fri Feb 03 2006 - 02:38:55 CST


Dear Carlos Simmerling


Thank you for advising me.

Then should I use sander module on amber8 manual,i.e. "Potenials of mean
force using umbrella sampling" and WHAM method ?

On this manual, it is said "These different simulations(often called
"windows") must have some overlap"

Does it mean that after one simulation is carried out, the next one should
be started at the structure caluculated by last simulation ?



A. Okabe



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