VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Apr 16 2006 - 17:23:42 CDT

Dear Rima,
this is usually best done using catdcd
(http://www.ks.uiuc.edu/Development/MDTools/catdcd/), which lets you
either split the dcd file into subparts or write only certain frames or
atoms from it. For the record, you're probably running your computer out
of memory; if you have a machine with enough memory VMD can open much
larger dcd files.

There are examples of catdcd usage on the linked page; please let me
know if you have trouble.
Best,
Peter

Rima Chaudhuri wrote:

> Hello!
> I have a 3GB DCD file at this moment, the frames were written at every
> 100 steps, the simulation is still running and is only 40% complete
> (of total 1ns). As of now it has some 4000+ frames. The huge DCD file
> cannot be uploaded in VMD, it reaches its memory limit and crashes. Is
> there a way I can break the DCD file into sub-parts and then upload
> it? or if there is any way around this problem?? Any help would be
> much appreciated.
>
> Thanks
> -Rima.
>
>
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