VMD-L Mailing List

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed May 03 2006 - 13:12:40 CDT

Thanks a lot!

On 5/3/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> 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
> 

--
---------------------------------------------------------------------------------------------
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.