soft-core potential for FEP

From: felmerino_at_uchile.cl
Date: Wed Apr 08 2009 - 17:46:33 CDT

Hey NAMD guys:

I am interested in the difference of affinity of an enzyme between ADP and ATP
so i decided to performe some FEP caculations to measure it. I started the issue
using NAMD 2.6 and , of course, i had some convergence issues around the ending
points. So, i tried the new NAMD with the soft-core potetials. I understand the
use of the van der Waals switching from the Beutler et al paper (chem phys lett
1994 222, 529-539) but i'm a little confused about the other two options
(elecstart and the wvw one). The default parameters seems to be somehow
execsive, i tried with the ethane-ethane zero sum FEP from the tutorial and the
best results were with a lower switching (value of 2) and electstart and vdw and
of 0.1 and 0.9 respectively. However i don't think a try and error way would be
useful for a bigger problem, so if anyone can guide me through the choise of the
appropiate parameters it would be a lot of help. Anyway, sorry about the
ignorance

Thanks in advance

Felipe

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