VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 06 2004 - 18:27:10 CST

In Mauricio's case, the DCD reader ought to be reading this information
in already, assuming it is present in his trajectory file and he's using
VMD 1.8.2. If its not in the trajectory file, then using a script is
definitely the next best thing if its available elsewhere.

  John

On Tue, Jan 06, 2004 at 11:49:44PM +0100, Axel Kohlmeyer wrote:
>
> >>> "MT" == Mauricio C Tripp <trippm_at_wabash.edu> writes:
>
> [...]
>
> MT> My next problem is that since I'm looking at a
> MT> NPT simulation, the box dimension will change from
> MT> frame to frame. Is there a way to modify the script
> MT> so it would set the correct box dimensions to
> MT> each frame and just not the same parameters for
> MT> the whole trajectory?
>
> i think the straightforward way would be to create a file
> which contains the required parameters, one set per frame,
> open the file and then read in the next set of parameters
> in each iteration of the loop. i don't have an example
> ready, but you may find some inspiration at
> <http://www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html>
> or in the vmd script library or a tcl reference book.
>
> take care,
> axel kohlmeyer.
>
> --
> =======================================================================
> Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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