AMBER Archive (2009)

Subject: [AMBER] Question about Thermal Integration with Softcore

From: Elodie Laine (
Date: Wed May 13 2009 - 04:13:22 CDT

Dear all,

I want to perform a FEP using the Thermal Integration functionality of
sander, with softcore. Instead of mutating my ligand (a calcium ion
actually), I simply want to make it disappear. Do I need to run the TI
steps (removing charges + removing vdW) on 2 processes V0 and V1, using
the "groupfile" option, in this case ? Or can I simply simulate one
process ?

Thanks in advance.

Elodie Laine

Pasteur Institute
Structural Bioinformatics Unit
25-28, rue du Dr Roux
75724 Paris Cedex 15
+33 (0)1 44 38 94 82

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