Re: rigid molecule

From: Felipe Merino (
Date: Sun Mar 28 2010 - 17:45:56 CDT


The RigidBonds options just control the bonds that involves hydrogen
atoms. If you want to restrict the conformation of your molecule (for
any reason) while it is still free to translate you can do that by using
a strong RMSD restraint to all the atoms of your molecule using and
harmonic restraint with the colvars module. If you use a high constant
the your molecule will be "stiff enough".


Mark M Huntress escribió:
> Hi, I would like to simulate the reorientation of a molecule inside a protein cavity, while keeping the molecule completely rigid- bonds, angles and dihedrals. It should only be free to translate and rotate. I tried rigidbonds all but that did not work, because it was still too flexible to move (the dihedrals). Does anyone know if there is a way to do this in NAMD?
> Thanks.
> Mark

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