Re: [AMBER] Separate work values for each restraint in SMD

From: Adrian Roitberg <>
Date: Wed, 16 Jan 2019 10:15:05 -0500

Hi, as is no, you cannot separate them.

If you go into the source code, it should be a one or two line change to
print it as you wish.

Also, if you save structures from the MD DUMPFREQ step (which I usually
do not recommend), you can always compute this yourself at the end of
the run, by computing the actual value of each coordinate vs 'time', and
what the expected value of that coordinate is (dx/nstlim, etc), and usin
gthe force constant you set in your RST file to compute the integral of
-k*dx for each coordinate separately

The value printed is NOT the average work, but rather the sum of all
works for all restraints


On 1/16/19 10:10 AM, Sundar wrote:
> Dear Amber Users,
> I am performing steered MD with multiple distance restraints.
> Does anyone know how to print Jarzynski's work value for each of the
> restraints separately?
> I am currently using DUMPFREQ and DUMPAVE, which only prints only one work
> value. I think that is an average for all the restraints.
> Any help would be appreciated.
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
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Received on Wed Jan 16 2019 - 07:30:03 PST
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