Still, to my knowledge, there is no analytical Hessian implemented anywhere
in sander or pmemd (can someone verify this?).
Getting a numerical Hessian can of course be done by finite differencing,
but at the expense of 3N or 6N additional force evaluations (N being the
number of atoms). It might be easier to do this by setting ntwr to a
negative value and regularly saving structures to be post-processed. Our
group set up a rather hasty set of Python scripts to do this and many of
the (decidedly more polished) core tools are or will be available in future
versions of AmberTools.
Regards,
Brian
On Tue, Aug 6, 2013 at 1:41 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> On Aug 5, 2013, at 6:26 PM, John Travers <jtravers70.yahoo.com> wrote:
>
> > Hi Brian
> >
> > Thanks for the note. If the do_debugf and dumpfrc options are turned,
> the program will just stop after one step. What I want to have is the
> cartesian forces throughout the trajectory? Thanks again!
>
> If you want this information, you will need to edit the sander or pmemd
> source code yourself to dump that information.
>
> I added a force dump option to the developer's version that will be
> released with Amber 14 next year, but there is no option to do that in
> amber 12.
>
> I recall writing 2 emails to the list in the past 2 or 3 months detailing
> how to do this, so you should be able to find those threads in the archives
> if you want some tips on where to start coding it yourself.
>
> HTH,
> Jason
>
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Tue Aug 06 2013 - 07:30:02 PDT
