VMD-L Mailing List

From: John Keller (jwkeller_at_alaska.edu)
Date: Mon Mar 25 2013 - 00:14:44 CDT

Does VMD have a way to prevent part of a molecule from rotating during
playback of a MD file? I am using VMD 1.9.1 to visualize a .xyz file from a
Gaussian ADMP MD calculation for a smallish, flexible molecule. For
example, unrestrained MD of ethylbenzene shows the whole molecule tumbling
about its center of mass. However, one would rather keep the phenyl ring
approximately level to better see the motions of the ethyl group relative
to the rest of the molecule. Alternatively, I suppose this could be done in
Gaussian at the outset of the calculation.