[gmx-users] settle for other solvents
feenstra at chem.vu.nl
Tue Feb 18 11:14:09 CET 2003
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
What about dummy atoms *with* mass? I think Berk explained to me once
why and how that is impossible...
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "The World is a Friendly Place" (Magnapop) |
More information about the gromacs.org_gmx-users