Re: [AMBER] single -step transformation TI calculation

From: <>
Date: Sat, 17 Dec 2011 05:46:21 -0500 (EST)


> issue you mentioned below). So I guess for a single-step transformation,
> the soft-core potential is probably still preferred even for the same
> number of atoms.

while individual results may vary, that is generally not true in my
opinion. The SC methods prevents a specific kind of instability that
occurs when creating/removing whole atoms. It does not automatically
improve convergence of your results. However, the way thing are
implemented now, switching on SC also allows you to make use of
dual-topology transformations, which may or may not help your simulation.
The crucial thing always will be to do statistically valid error analysis
and closely look at your free energy curves. Those are the true indicators
of free energy result qualities.

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Sat Dec 17 2011 - 03:00:03 PST
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