VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Tue Jan 06 2009 - 17:25:03 CST

Dcd files can be very easily manipulated with catdcd tool. For example, you
can extract every 100th frame, you can select first and last frames and
thus split the original trajectory into several sub-trajectories.

http://www.ks.uiuc.edu/Development/MDTools/catdcd/

On Tue, Jan 6, 2009 at 5:31 PM, <jouko_at_berkeley.edu> wrote:

> I am trying to convert a dcd file that is larger than 7 GB to individual
> pdb files. When I run the script I normally use to convert dcd files to
> pdb files vmd aborts. The script is pasted below.
>
> mol load psf ubq_solution_wb.psf dcd ubq_wb.12ns.dcd
> set nf [molinfo top get numframes]
> for {set i 0} {$i<$nf} {incr i} {[atomselect top all frame $i] writepdb
> /home/jouko/1ubq_phosphate5/0-3_ns/ubq_$i.pdb}
>
> I was thinking that the dcd file might be too large to be read by vmd, so
> I thought I could split it up using sed. However when I do that vmd is
> not able to read the split up dcd files, except for the first one. Any
> help would be appreciated.
>
>
> Thanks,
>
> Jouko
>
> 

-- 
Roman Petrenko.
Physics Department
University of Cincinnati