O.k Cheers Justin A. Lemkul wrote: > > > 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 >
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