VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Mar 14 2008 - 09:49:00 CDT

On Fri, 14 Mar 2008, Christopher Stiles wrote:

hi christopher,

CS> I am currently using VMD to analyze single wall carbon nanotube simulations
CS> (swcnt).

CS> I have done 3 sets of runs varying temperature with each set using Gromacs.
CS>
CS> The first with a (6,6) swcnt with an output *.trr of 2.86gig
CS>
CS> The first with a (10,10) swcnt with an output *.trr of 4gig
CS>
CS> The first with a (20,20) swcnt with an output *.trr of 8gig
CS>
CS> I have noticed when I go to load them into vmd I get different numbers of
CS> frames even though every simulation was run using the same time step and
CS> same number of steps, giving 10ns runs.

did you check the gromacs log files, whether the jobs have
completed correctly? assuming that each system has about
the same number of atoms, you should get the same disk
usage with .trr format. it is not a compressing file format.

[...]
 
CS> So my question, is there a limitation on the data size that can be
CS> read into the windows version of VMD? Or is there some other

if i remember correctly, the windows version supports only up
to 2GB of memory usage. but i don't use windows, so i don't know
for sure. please check out the windows specific VMD release notes
on the VMD homepage.

CS> limitation that I am not aware of? I seems to me that the *.trr
CS> files increase in size in proportionate amounts in relation to there
CS> total number of atoms to contain equal amounts of frames.

yes. .trr stores 12bytes per atom per frame (counting positions
and velocities independendly).

cheers,
    axel.

CS>
CS>
CS>
CS> I appreciate any input on this matter!
CS>
CS>
CS>
CS> Thank you very much!
CS>
CS> ~Christopher Stiles
CS>
CS> College of Nanoscale Science and Engineering (CNSE)
CS>
CS> State University of New York, Albany, New York 12203, USA
CS>
CS>
CS>
CS>
CS>
CS> 

-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.