[gmx-users] virtual sites set up for topology file

Justin A. Lemkul jalemkul at vt.edu
Fri May 6 14:19:46 CEST 2011

Gavin Melaugh wrote:
> Yeah I see your point about the types. With regard to the initial
> configuration state I would have assumed that gromacs knew the initial
> position of the virtual site  when I stated that it was to be at the
> COG  of the  3 atoms in  the [virtual_sitesn] directive.

I believe this information is only used during mdrun to construct the position 
after forces have been applied and coordinates updated.  You can run a simple 
protein through pdb2gmx with -vsite hydrogens to see how all of this should be 
put together.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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