[gmx-users] pdb2gmx and virtual sites

Ondrej Marsalek ondrej.marsalek at gmail.com
Thu Nov 5 13:07:12 CET 2009

On Wed, Nov 4, 2009 at 21:54, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> "For the remaining degrees of freedom, the shortest oscillation period
>> as measured from a simu-
>> lation is 13 fs for bond-angle vibrations involving hydrogen atoms."
>> And then later on in section 6.5.1:
>> "The goal of defining hydrogen atoms as virtual sites is to remove all
>> high-frequency degrees of
>> freedom from them."
> The quotes above define the problem, but I see no reference to using
> h-angles as your constraints.


>> As far as I understand the procedure, the hydrogens can only be
>> converted to virtual sites if the angles are constrained, because only
>> then is their position uniquely given by the positions of heavy atoms.
> See the following:
> http://lists.gromacs.org/pipermail/gmx-users/2008-October/037569.html

Thanks for the pointer, it seems to work that way.

Thank you for your help,

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