VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue May 27 2008 - 12:54:41 CDT

craig,

please don't crosspost to lists where the bisection of subscribers is small.

On Tue, May 27, 2008 at 11:53 AM, Craig Maloney <craigmaloney_at_cmu.edu> wrote:
> Hi all.
> I'd like to do some post-processing which involves, e.g., assembling the
> full trajectory for an arbitrary particle in my system. I keep the dumped
> output of my entire MD run in a single dump file which is too big to fit
> into system memory. With ascii-based output (e.g. LAMMPS default or custom
> dump), assembling a single-particle trajectory is a slow operation, since
> the code needs to read line-by-line, so the run time scales like
> numAtoms*numTimesteps even if I just want to look at the first atom. I
> figured there would be some binary based format, e.g. DCD, which would be
> much more amenable to this kind of post-processing. I'd like to work in

using VMD and a tool/script called bigdcd is probably the way to go.

you only load the trajectory frame by frame and VMD can handle .dcd and .xtc
binary trajectories (no LAMMPS binary, yet).

i also have a hack that allows writing .dcd files of a LAMMPS group
and thus would allow this kind of processing during the LAMMPS run
(unless you need a more complicated way to select the atom).

cheers,
    axel.

> python if possible but that's not strictly necessary.
> There is MDTools (http://www.ks.uiuc.edu/Development/MDTools/Python/), but
> it looks like it can only read all particles for a single given DCD frame,
> rather than tracking a single particle for all frames. I might be wrong,
> but this is the impression I get when glancing at the docs. Am I right?
> I just came across MDAnalysis: http://code.google.com/p/mdanalysis/
> Anyone have any experience with it? Will it assembly single-particle
> trajectories from a DCD file (or other binary format) in reasonable amounts
> of time (order numTimesteps rather than order numAtoms*numTimesteps)?
> Thanks,
> Craig
> -----------------------------------------------
> Contact info:
> http://www.ce.cmu.edu/~maloney2/
>
>
>
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-- 
=======================================================================
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.