Re: Superimposed trajectory

From: David A. Case <>
Date: Tue, 10 Jun 2003 07:53:42 -0700

On Tue, Jun 10, 2003, Filip Razga wrote:
> My problem : I want to do a trajectory , which every one snapshot is
> mass fitted to the first or reference snapshot, thats mean that the
> molecule will be superimposed every snapshot to the reference-by using
> Ptraj and create a superimposed trajectory without the rotation of the
> molecule.The trajectory will stored the coordinates of the fitted
> structure every time step-something like mass weight fitted rmsd, but
> without calculating the rmsd values, only stored the fitted coordinates.

The "rmsd" command in ptraj does what you describe above. You can ignore the
rmsd values if you wish, and just use the superimposed trajectory for
other analysis.

...hope this helps....dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Tue Jun 10 2003 - 16:53:02 PDT
Custom Search