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 - 12:00:03 PDT
