[gmx-users] settle for other solvents

[Anton Feenstra]

David van der Spoel wrote:
> 
[...]
> You define the settle plane to be O-Me-Me and have the S as a dummy.
> Then you reshuffle the mass of the S over the three atoms until the
> moment of inertia is the same... Slightly easier, but still not
> one-to-one mapping I'm afraid...

This is very similar to what I did for dummified (i.e. no internal
degrees of freedom) -NH3/-CH3 groups, or for a dummiefied tryptophane
ring. At least for the -NH3/-CH3 case there is more or less general
code to calculated the redistributed masses. I don't remember if that
went indo pdb2gmx or grompp, in any case it must be in either dum_parm.c
or gen_dum.c (src/kernel). Maybe you can re-use some of it...

For a planar molecule like DMSO, I suspect it should be possible to get
the mass distribution such that its properties are identical to the
'normal' version. Not sure about it, though, it depends I think on the
moments of inertia in *all* possible directions (not just three principal
axes).

What about dummy atoms *with* mass? I think Berk explained to me once 
why and how that is impossible...



-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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