Re: [AMBER] How to modify the formula for non-bonded interactions

From: Jason Swails <>
Date: Mon, 22 Jul 2013 14:55:08 -0400

On Mon, Jul 22, 2013 at 2:17 PM, Pengzhi Zhang <>wrote:

> Hi,
> I am using Amber 10 sander to run molecular simulations. Now I want to do
> some tests on different ways to mimic van der Waals interactions. As far as
> I know, in amber, 6-12 Lennard Jones potential is used. Does anyone know
> whether I can make some modification to this potential, such as making it
> to
> 6-10-12 potential? Any help is appreciated.

The only way of doing this is by modifying the Amber source code. Have a
look at where the non-bonded interactions are computed in sander
(subroutine get_nb_energy in short_ene.F90 for PME in sander, egb.F90 for
GB in sander, gb_ene.F90 for GB in pmemd, and somewhere inside
get_nb_energy in pmemd (I'm not sure about the latter, since Amber 10 is
quite old and I don't have ready access to that version of the source code).

Especially when asking about source code modifications, it's probably best
to use the most up-to-date version of Amber available, or the number of
people that will be able to answer your questions will be limited.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jul 22 2013 - 12:00:04 PDT
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