VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Mar 25 2013 - 01:42:46 CDT

On Mon, Mar 25, 2013 at 6:14 AM, John Keller <jwkeller_at_alaska.edu> wrote:
> 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.

in general, it usually is preferable to have a weak position restraint
for this, since doctoring up the trajectory data after the fact may
lose important information. but you *can* do that with VMD using the
RMSD trajectory tool which allows you to do a fit of a selection of
atoms to a reference configuration. it also is possible to do what you
want by adjusting the camera position during viewing of a trajectory.
check out section 6.2 in this document:
https://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1

the latter option, like using a weak position restraint, has the
advantage to result in a smoother visualization. using a fit can
result into quite strange motions, similar to a "shakycam",
particularly for larger molecules.

HTH,
    axel. 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.