[gmx-users] Switching off Hbonds

David spoel at xray.bmc.uu.se
Tue Jan 27 17:16:02 CET 2004

On Mon, 2004-01-26 at 14:23, Anton Feenstra wrote:
> Sandeep Somani wrote:
> > Hi 
> > 
> > Is there a way to selectively switch off a particular hydrogen bond
> > during a simulation, say between an OH group of a Tyrosine and a
> > carbonyl oxygen ?
> No - hydrogen bonds are not added explicitly, but rather result from the
> combination of electrostatic and vanderwaals interactions. However, you
> may get the desired result by removing charges from the atoms involved
> in the h-bond. That will also have other effects, though. Alternatively,
> you might add a 'repulsive' distance restraint (i.e. using the lower-
> bound parameter) to counteract the attractive interaction of the h-bond.

or try the energy exclusions. be prepared that the groups won't see each
other anymore (and may overlap as a result)

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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