Dear Ross,
Thanks for the reply. I had hoped it'd be an easy fix like the list
filtering you proposed. However, I had not given thought to the reciprocal
space, I have to figure that one out. I do all my simulations with PME.
Jose
On Tue, Aug 2, 2011 at 2:57 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jose,
>
> > I was wondering if one can switch off pairs of non-bonded interactions.
> > In
> > particular, I want to switch off the electrostatic interaction between
> > solvent and protein atoms, while leaving unchanged this type of
> > interaction
> > between protein atoms and between water atoms. Is this possible in
> > Amber?
>
> This is not currently supported in the input files however it would be a
> fairly easy modification of the source code to hard wire this as required.
> To do it for GB or non PME calculations would be fairly simple, where the
> charge charge interaction is calculated you just have an if statement that
> checks what the atoms are in the atom pair. You could even do it at the
> list
> build stage for PME runs and remove interacting pairs that you do not want
> from the list. Water would be easy to identify since it is the only atom
> that has type OW or HW. But other approaches could be used including
> looking
> at the atom type etc.
>
> One could even quite easily put together a mask for this and use the
> standard mask passing routines in Sander.
>
> Note having if statements inside the direct space loops my hurt performance
> a bit but putting it in the pair list generation step would only hurt every
> 10 steps or so.
>
> For PME things will get a bit trickier since you will have to work out how
> to screen the interactions in the reciprocal space as well as the direct
> space. Have you actually considered how one would actually do this in
> practice? It will take some thinking about the underlying maths to get that
> correct before actually modifying the code.
>
> Good luck,
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Tue Aug 02 2011 - 13:00:02 PDT
