VMD-L Mailing List

From: bo liu (liubo.njuer_at_gmail.com)
Date: Fri Oct 17 2008 - 00:01:59 CDT

Hi Christopher,

In your case, one thing you can do is to load the DCD with a stride of 2.
then you can have a "whole picture" of your simulation without running out
of memory resources.

Cheers!
Bo Liu
2008/10/17 Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>

> On Thu, 16 Oct 2008, Christopher Hartshorn wrote:
>
> christopher,
>
>
> CH> Is catDCD in VMD? I can not find it in extensions menu. I need to cut
> a
>
> catdcd is a standalone executable. it should be in the plugin tree
> somewhere
> under $VMDHOME/plugins/<insert platform here>/bin/catdcd4.0/catdcd
>
> CH> 3.4GB .dcd file into 1/2s, I think, because it continually crashes VMD
> CH> around the 700/1000 frames. Any help would be appreciated.
>
> why not tell VMD to load only 500 frames. You have an option to set.
> the first, last and stride of frames that you want to load.
>
> and then (later) load the other 500.
>
> if your VMD session crashes because of running out of memory,
> you won't have any gains from splitting the file into two
> pieces and loading them seperately anyways.
>
> cheers,
> axel.
>
>
> CH>
> CH> Best,
> CH> Christopher Hartshorn
> CH> WSU
> CH>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> 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.
> 

-- 
-Liu bo
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