VMD-L Mailing List

From: Jeff Taylor (jstaylor_at_duke.edu)
Date: Tue Jul 31 2001 - 10:19:39 CDT

Mauricio Carrillo-Tripp wrote:
>
> Hi, i would like to know if it is possible to do the following:
> I'm displaying a MD run from a dcd charmm file. The problem
> is that as the run pass by, the molecule rotates randomly.
> I would like to fix a certain atom on the origin, another on the
> x axis, and a third one on the x-y plane, in such a way that
> those three atoms are always on a fixed plane so when I play
> de MD the molecule wont rotate.
> Or, is there another way for fixing it?
> thank you.
>

Probably the easiest way is to go back to charmm and use the coor orient
command to re-orient your tradjectory. This is a standard task that is
outlined in the charmm docs.

Here's a section from the "dynam.doc":

                   Reorienting a coordinate trajectory

      If one is interested in reorienting every set of coordinates
found in a dynamics trajectory with respect to some reference structure,
one can use the ORIEnt option in conjunction with the MERGe command.

      The process of reorienting a coordinate trajectory works as
follows: A series of files containing the trajectory are assigned to
successive units prior to a CHARMM run. The coordinates stored therein
are presumed to have been written every NSAVC steps. CHARMM will read
each coordinate, select some periodically, reorient them, and write them
to successive units where each output file will have a user specified
number of coordinates. The following table lists the options involved:

Option Default Purpose

ORIE .false. Specify that a least squares RMS fit will be
done.
MASS .false. Use a mass weighting in the fit
WEIGH .false. Use the weighting array (wmain) in the fit
NOROt .false. Just shift the centers to best fit.
PRINt .false. Print what happened to each coordinate set.
atom-selection all Select which atom to use in the fit.

      If atoms were fixed during the dynamics, the new trajectory
produced will not have fixed atoms because the rotations applied to
each coordinate set will be different thereby yielding different
coordinates for the fixed atoms. Fixing the coordinates leads to a
large space reductions, so the reorientation process will therefore
result in potentially much larger trajectory files.
See *note fix: (chmdoc/cons.doc)Fixed Atom.

- Jeff Taylor 

-- 
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Dr. Jeffrey S. Taylor       Duke University Medical Center
Department of Biochemistry  Box 3711, Nanaline Duke Bld  
Phone (919) 681-5266        Durham, NC 27710