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

From: Ross Walker <>
Date: Thu, 8 Dec 2011 08:59:14 -0800

Hi Marc,

> 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?

I have asked this question myself many times. It rebuilds the list to be
able to deal with extra points. But WHY? I have been burnt by this myself
many times - I still get burnt by it but to be honest it will make you grey
trying to understand why things like this are done - Obviously doing it is
fine BUT it should have been done completely, with the exclusion list being
completely removed from the prmtop and the 'original' path in the code also
being removed.

> 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

The lesson here is one I try to teach to anyone coming into computational
chemistry and molecular dynamics. You have the source code. The best and
most powerful approach is to get yourself familiar with the code, at least
some of it. What you want to do is VERY simple by just editing the code, far
more simple than trying to mess with a fragile prmtop. A few lines is all
you need to turn off non-bond interactions and would take 5 to 10 mins at

> 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.).

Agreed, in principal. But it needs everyone to appreciate this. The problem
arrises from the fact that the original prmtops were not extensible. Hence
it was difficult, near on impossible, to make modifications to the prmtop,
add new features to the prmtop etc and so people took short cuts elsewhere.
These work but ultimately come back and bite people.

That said though, what you want to do, turn off the non-bond interactions
should be a setting similar to the cutoff - not hard coded in the prmtop.
Thus I believe the correct approach here is to edit the code and add a
switch there rather than messing with the prmtop.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Thu Dec 08 2011 - 09:00:02 PST
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