[AMBER] free energy calculation with TI

From: Dian Jiao <oscarjiao.gmail.com>
Date: Tue, 15 Mar 2011 14:55:04 -0600


I am following this tutorial below and tried to calculate solvation free

Here are some questions I have regarding the table towards the bottom on the
same tutorial webpage:

1. Step 1: removing charge on H6 of BNZ. The input file difference between
V0 and V1 is the crgmask (except for clambda). What about intermediate
steps? Should I use the same crgmask as V1, so that AMBER would know what
atoms are associated with clambda transformation?

2. Similarly, what are crgmask and scmask supposed to be for the
intermediate steps with clambda ranging from 0.1 to 0.9? And which prmtop
file should these substeps be using?

3. For solvation free energy calculation, is one prmtop file enough for both
charge-removing and vdw-removing if softcore potential is applied?

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Received on Tue Mar 15 2011 - 14:30:02 PDT
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