Re: loading large dcd files

From: Axel Kohlmeyer (
Date: Thu Jan 29 2009 - 09:03:44 CST

On Thu, 29 Jan 2009, sripad chandan wrote:

SC> Dear Friends,
SC> I have run a 10 ns (10 thousand frames) simulation in 5 steps of 2 ns each.
SC> Now I want to merge the files.
SC> The total volume of files is above 2GB.
SC> I just first loaded the psf file and then the dcd file one after another.
SC> but after loading about 7500 (7.5 ns) frames the vmd is crashing.
SC> I am using VMD 1.8.6 on windows xp platform on a PC of 2 GB RAM.
SC> is there any error in dcd file?

no, but the problem is in windows. the VMD windows builds are 32-bit
and thus the total memory it can use is limited. i don't know exactly
how much, but it has to be less than 2GB, recent VMD builds should
actually print out how much memory VMD has available.

but then again, i don't quite see the need to combine those files to
begin with. large files are a nightmare to manage, are prone to
corruption (disks do occasionally have errors, and would you rather
want to lose one big file with your whole trajectory, or a small
portion of it), and with tools like VMD you can always load multiple
segments via a few script commands as if it were one big trajectory.

for analysis you can do even better: there is the bigdcd script that
allows you to process a near infinite size trajectory transparently
by handling one frame a time.


SC> hope I ll get some help.
SC> thanks in advance.
SC> chandan

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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