Re: [AMBER] Question about AMBER energy decomposition

From: Lee-Ping Wang <>
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.


- Lee-Ping

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

From: "Jason Swails" <>
To: "AMBER Mailing List" <>
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 <> 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 M. Swails 
Rutgers University 
Postdoctoral Researcher 
AMBER mailing list 
AMBER mailing list
Received on Sat Jul 04 2015 - 07:00:02 PDT
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