Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms?

From: Marc van der Kamp <>
Date: Thu, 8 Dec 2011 14:43:28 +0000

> > It appears that igb=0,eedmeth=4 does not obey the exclusion list, but
> > igb=6 does. (When I add bonds, angles, and a dihedral to the system,
> > igb=0,eedmeth=4 does properly exclude each atom from the non-bonded
> > calculation list).
> I think the code path followed by igb=0 recomputes the exclusion list based
> on the bond list. This illustrates one of the dangers in
> hand-modification of prmtop files: there may some hidden assumptions about
> the prmtop data that are not obvious just from a description of the file
> format.
I can see one can argue that this is the danger of (hand) modification of
prmtop files.
On the other hand, why does igb=0 (i.e. the ewald code for the EEL/VDW
calculations) recompute the exclusion list based on the bond list?
Is this for efficiency reasons?
If not, wouldn't it be better to make the ewald code for the EEL/VDW
calculations use the exclusion list as defined in the prmtop?
First of all, this does make it very tricky (near impossible?) to turn off
non-bonded interactions between non-bonded atoms without changing the
source code. (In principle, one could add bonds with 0 force constants
between all the atom pairs for which one wants to turn off the non-bonded
interactions, but this is going to hurt efficiency, especially with large
numbers of such atom pairs)
Second of all, it would be nice if simulations actually *do* use what is
defined in the prmtop. This is what is nice about having a prmtop - it
defines, in principle, the basic energy function used for the system
(admittedly without things like boundary conditions, cut-offs, implicit
solvent models etc.).


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Received on Thu Dec 08 2011 - 07:00:02 PST
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