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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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