Re: [AMBER] Question about AMBER energy decomposition

From: Lee-Ping Wang <leeping.stanford.edu>
Date: Sat, 4 Jul 2015 06:41:04 -0700 (PDT)

Thanks, Jason; I did something similar where I created a separate set of parameter files that zeros out the improper torsions; that allows me to isolate the improper torsion contribution to the energy. :)

Since this was just for verifying the correctness of the AMBER-FB15 parameter conversion, it didn't have to be efficient.

Thanks,

- Lee-Ping

----- Original Message -----

From: "Jason Swails" <jason.swails.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Friday, July 3, 2015 2:30:00 PM
Subject: Re: [AMBER] Question about AMBER energy decomposition

On Fri, Jul 3, 2015 at 3:28 PM, Lee-Ping Wang <leeping.stanford.edu> wrote:

> Hi everyone,
>
> I'd like to know whether sander has the ability to separate the proper and
> improper dihedral energy contributions in the output file. Thanks a lot!
>

‚ÄčNo it can't, since they're all included in the same potential list (at
least to my knowledge). We can add this to ParmEd-OpenMM, though.
Basically, just have omm_dihedral_force return two forces -- one containing
*just* the improper periodics and another containing *just* the proper
torsions. (Structure already knows how to handle a function returning
multiple Force objects, since the omm_nonbonded_force often has to do this).

We can chat a bit more about this on the ParmEd issue tracker as well if
this is the route you want to go.

All the best,
Jason

-- 
Jason M. Swails 
BioMaPS, 
Rutgers University 
Postdoctoral Researcher 
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Received on Sat Jul 04 2015 - 07:00:02 PDT
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