VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Tue Sep 13 2005 - 10:20:35 CDT

I do this routinely with a script of the form:

mol new mol.psf
animate read dcd file.dcd beg 0 end 1999 waitfor all top
set temp [atomselect top "segname X Y Z"]
animate write dcd nosolvent.dcd beg 0 end 1999 waitfor all sel $temp top

Chris

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of dimka
> Sent: Monday, September 12, 2005 7:34 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: dcd tools
>
> Dear all, is there a way to rewrite a DCD file minus the solvent?
>
> I'm aware of a catDCD tool, but i was thinking more on the
> lines of something more intuitive:
>
> after vmd reads you psf and dcd file do something like this:
>
> set sel [atomselect top protein]
> $sel writedcd -from 1 -to 100 protein.dcd
>
> this way it is easier to analyze longer trajectories...
>
> sincerely,
>
>