From: Anthony Cruz Balberdi (
Date: Tue Apr 09 2013 - 10:00:24 CDT


You should use bigdcd ( ). You
could do a script that do exactly that and without memory problem since
bigdcd load one frame at a time (Check the examples). If you need help let
me know...

Best Regards,


On Mon, Apr 8, 2013 at 7:42 PM, Yarrow Madrona <> wrote:

> Hello,
> I am trying to convert a dcd to a series of pdb's without opening the VMD
> GUI. The reason is that I don't have enough ram to store the DCD (70,000
> frames) into memory. VMD always crashes unless I use a truncated DCD. I
> would like to use all frames since the frames will be analyzed by another
> software (Caver3.0). Is there a way to tell vmd to write out all PDBs in
> the command line (preferably without water although I can remove those
> later)?
> Thank you
> --
> Yarrow Madrona
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697