[gmx-developers] genvsites

[Erik Marklund]

Hi,

I've put some text on the wiki for genvsites (http://wiki.gromacs.org/ 
index.php/Genvsites) describing the current state of things. We've  
decided to make a force field independent description of the virtual  
site constructions, which does not contain much geometrical nor  
topological information. Ideal geometries will be constructed from  
refi_aa.dat, containing crystallographic bond/angle/tortional data,  
from which in turn center of mass and moment of inertia will be  
calculated when needed. We're aiming to make the program 'stupid',  
i.e. not make too many assumptions or smart decisions, and just read  
and interpret the vsite data file. Some information will be taken  
from the topology, and perhaps also from the force field in special  
cases. Any comments on the proposed file format or the overall  
strategy is greatly appreciated.

Over and out.

_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys


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