AMBER Archive (2002)

Subject: Re: entropy calcs in mm_pbsa

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue Nov 05 2002 - 15:27:39 CST

Hi,

> 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)?
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

Holger 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
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
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++