Re: [AMBER] turning of non-bonded interactions with addExclusions

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 4 Apr 2016 12:10:09 -0400

On Mon, Apr 4, 2016 at 5:42 AM, Batuhan Kav <bkav13.ku.edu.tr> wrote:

> Dear All,
>
> I have a system with two carbohydrate molecules, each consists of four
> residues. I basically want to turn off all the non bonded interactions
> between these two molecules. For that, I use parmed with the following
> command (after loading the original prmtop file)
>
> addExclusions :1-4 :5-8
> outparm new.prmtop
>

​This is somewhat risky. In sander and pmemd, this *only* works when using
the GB code path to calculate electrostatics. Which means it can't be used
with PME or periodic boundary conditions in sander or pmemd. To do a gas
phase calculation (i.e., with no GB model), set igb=6 in the &cntrl
namelist. Then you should see a difference.

This happens because sander and pmemd "recompute" the nonbonded exception
parameters from the list of bonds, angles, and torsions rather than using
the one stored in the prmtop file. I had written the "addExclusions"
action before I figured this out.

If you need these exclusions in a PME calculation, you'll need to use
another program that *does* respect these additional exclusion rules. For
example, OpenMM (which you can access via the "OpenMM" command in ParmEd to
run a sander-like simulation).

HTH,
Jason

-- 
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 04 2016 - 09:30:04 PDT
Custom Search