RE: Re: vmd-l: breaking the DCD file

From: Pijush Ghosh (
Date: Sun Apr 16 2006 - 19:35:18 CDT

Hi Rima

Do you need all the frames to be there? I mean every single step..if that is
the case, then use catdcd to break your big dcd files to a smaller ones and
then you can load it on vmd, if you don't need all these then just store
your dcd files every 1000 or 2000 steps as suggested by Snoze.

Let me know if I have further confused you.




Pijush Ghosh

PhD Student

Department of Civil Engineering

North Dakota State University

Fargo. ND. 58105. USA





From: [] On Behalf
Of snoze pa
Sent: Sunday, April 16, 2006 5:09 PM
To: Rima Chaudhuri;
Subject: namd-l: Re: vmd-l: breaking the DCD file


 to avoid this situation try write output in every 1000 steps. this will
reduce your dcd file size.

On 4/16/06, Rima Chaudhuri <
<> > wrote:


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.




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