> I dealt with this problem a couple of days ago in mdgx and had to fix
> the
> zeros by intercepting them as I populated the list of the scaling
> factors
> actually implemented in the calculation. I make a list of "adjustment"
> factors for 1-4 scaling terms, which are basically 1 - 1.0/T where T is
> the 1-4 term read in from the topology. When T is zero I make T=1.0,
> so
> that the adjustment term comes out to be zero and the overall effect is
> that the 1-4 interaction is unchanged. So, as far as I'm concerned I
> have
> dealt with this issue. But, it would seem simpler to designate "1.0"
> in
> the topology where a 1-4 bonded term is not meant to be scaled.
But what's the issue with just dividing by zero? Since the actual element of
the array should never be used. Unless you calculate all the dihedral terms
and then multiply any duplicates by zero.
Either way I think having the scaling term for all impropers and duplicate
dihedrals set to 0 is the best approach since then it will catch any
implementation that might be double counting 1-4s by mistake.
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 Fri Aug 12 2011 - 11:30:03 PDT
