Re: entropy calcs in mm_pbsa

From: Holger Gohlke <>
Date: Tue 05 Nov 2002 13:27:39 -0800


> 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:
> MAXCYC 5000
> DRMS 0.1
> Is there any particular reason for this? Or should I use vacuum electrostatics
> (DIELC=1)?
The distance-dependent dielectric is used to mimic (as best as is
possible in this case) the influence of a solvent during the
minimizations (so hopefully you get minimum structures which do not move
too far from the ones seen in explicit solvent).

> Is a DRMS of 0.1 enough for "reasonable" estimates?
No, this value was only set to speed up the example calculations. You
should set a value of DRMS=10^-4 kcal/(mol*A) or even below. It might be
necessary to also adjust MAXCYC then.

Best regards


Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
Received on Tue Nov 05 2002 - 13:27:39 PST
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