Re: [AMBER] internal energy in TI decomposition

From: Jason Swails <>
Date: Tue, 28 Jan 2014 07:01:24 -0500

On Tue, 2014-01-28 at 10:18 +0100, Schackert Nico wrote:
> Dear AMBER users,
> I'm performing TI calculations in Amber12 with energy decomposition
> (idecomp=1). Van der Waals and electrostatics contributions are fine,
> but I do not get any internal energies; all values in that column
> remain 0.
> Is there anything I'm missing? Setting RRES seems to only cause
> troubles with group numbers and residues therein.

The manual says "All residues, including solvent molecules, have to be
chosen by the RRES card to be considered for decomposition." so I would
suggest changing the bottom of your input file to:

decomposed residues
RRES 1 6904
printed residues
RES 1 6904

If something doesn't work, it would help to know specifics in order to
try helping.

Also, the idecomp flag means something different in standard simulations
than it does with TI. When running TI, the decomposed energies reflect
dV/dlambda, not the total decomposed potential. Indeed, I would expect
most of the internal terms to be 0, but a small number to be non-zero
(depending on how far the 1-4 nonbonded interactions extend from your
softcore mask).

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 28 2014 - 04:30:03 PST
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