[gmx-developers] position restraint algorithms

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 23 11:02:46 CEST 2008


in the latest development code the position restraint routine is treated 
differently from other bonded-force routines, because of possible 
communication requirements. However, this is only necessary when 
restraining the center of mass (COM) of a group of atoms, isn't it? An 
alternative implementation could use the COM vsite and restrain that. In 
that case the complexity is moved somewhere else, but posres gets cleaner.

I'm asking because I would like to implement a position-dependent force 
on the COM of a molecule. The force should in the end be tabulated 
rather than analytical, and hence I can re-use most of the mechanisms 
for tabulated bonds (except I need to add a one-particle table type). 
Any suggestions?

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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