VMD-L Mailing List

From: Christopher Stiles (CS145331_at_albany.edu)
Date: Fri Mar 14 2008 - 10:59:50 CDT

Thank you Axel!

>-----Original Message-----
>From: Axel Kohlmeyer [mailto:akohlmey_at_cmm.chem.upenn.edu]
>Sent: Friday, March 14, 2008 10:49 AM
>To: Christopher Stiles
>Cc: vmd-l_at_ks.uiuc.edu
>Subject: Re: vmd-l: different numbers of frames even though...
>
>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.
>
>[...]

All the jobs completed correctly, and each box is the swcnt plus 1nm of
padding (ie if you take the x,y,z dimensions of the swcnt and add 2nm you
get the box dimensions) and each box is filled w/ water so the larger the
nanotube the greater the number of atoms in the box.

>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.
>

I just checked this out and it makes not mention of memory limitations

>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).

Very good, this only makes sense, but it is good to know the actual size
thank you!

~Chris

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