VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 03 2006 - 12:38:43 CDT

Hi,
  You can do this by running VMD in text mode with
    vmd -dispdev text
(still interactive), or in a pure batch mode with
    vmd -dispdev text -eofexit < input.tcl > output.log

  John

On Wed, May 03, 2006 at 12:55:25PM -0400, Gustavo Seabra wrote:
> Hi all,
>
> A friend of mine is trying to use VMD to calculate the RMS of hundreds
> of thousands of structures. The structures are in pdb files, where the
> first structure is the reference, followed by a alrge,large,large
> number of structures.
>
> She can do it using a VMD script, but VMD is rendering every one of
> the structures, so it takes several hours (>8h!!) per file.
>
> We were wondering if there is a way to do this without rendering every
> frame.All she's interested is in the RMSD values, in a table. Maybe
> some command line tool?
>
> --
> ---------------------------------------------------------------------------------------------
> Gustavo Seabra Postdoctoral Associate
> Quantum Theory Project University of Florida
> Registered Linux user number 381680
> Say NO! to software patents: http://www.nosoftwarepatents.com
> ---------------------------------------------------------------------------------------------
> If at first you don't succeed...
> ...skydiving is not for you. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078