AMBER Archive (2002)

Subject: entropy calcs in mm_pbsa

From: giulio_at_unimo.it
Date: Tue Nov 05 2002 - 14:21:00 CST

Dear all,
I am performing free energy calculations using mm_pbsa. In particular, the
entropy component has been calculated for each snapshot of the trajectory, by
setting NM=1.
I noticed that in the sample input file, a distance-dependent dielectric
is used for NM:

DIELC 4
MAXCYC 5000
DRMS 0.1

Is there any particular reason for this? Or should I use vacuum electrostatics
(DIELC=1)?
Is a DRMS of 0.1 enough for "reasonable" estimates?

Thanns for your suggestions...
Giulio

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