Thanks for the suggestion.
The printed four column file had the following,
1.80000 12.12760 -41.31041 0.00000
1.80000 12.12760 -41.31041 0.01487
1.79964 12.12513 -41.30381 0.02974
As I understand from the user guide example in SMD section,
1st column is the instantaneous distance value of the restraint (may be the
first one of my 5 restraints?) and 4th column is the work value (as you
said the mean of all work).
What do the 2nd and 3rd columns mean? It would be great if some headers are
printed out.
Thanks,
J
On Wed, Jan 16, 2019 at 9:15 AM Adrian Roitberg <roitberg.ufl.edu> wrote:
> 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
>
> adrian
>
>
> 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
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks,
Sundar Thangapandian
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Received on Wed Jan 16 2019 - 08:00:05 PST
