[gmx-developers] suggestion: velocities.xtc

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Oct 17 10:26:52 CEST 2006


Actually, I did modify GMX3.3.1 to write velocities to a .xtc file
and, although I do agree with the statements regarding the offsets and
the need for precision, I find that there is definite benefit of using
the .xtc format. The file is much smaller than a .trr file (using the
same precision as for the positions, three decimals), although twice
as large as the coordinate .xtc file.



On 10/17/06, Erik Lindahl <lindahl at cbr.su.se> wrote:
> Hi,
> On Oct 16, 2006, at 6:50 PM, Jochen Hub wrote:
> > Dear developers,
> >
> > there are several applications around for which the velocities in
> > the simulation are interesting.
> >
> > Therefore it might be interesting if mdrun would allow optional
> > output of the velocities in xtc format. Using the trr file for
> > velocity analysis is usually not convenient since it simply gets
> > too large when writing to it in frequent steps. Probably it would
> > be relatively little effort so implement this with all the xtc
> > routines at hand. Of course, one mdp option like nstvxtcout would
> > have to be added, too.
> >
> > Have you ever intended to implment something like this?
> Unfortunately it isn't possible to compress velocities the same way
> as coordinates.
> First, for coordinates it is normally more than enough to save three
> decimals, while analysis of velocities at equilibrium usually require
> greater precision.
> Second, a key property of coordinates is that we can write them as
> offsets from the previous atom, which is particularly efficient for
> water that often makes up most of the system. This is not possible
> with velocities.
> So, while it would of course be technically possible to include v(t)
> in the xtc trajectory, the resulting file would end up very close in
> size to the normal trajectory. We are looking into alternative
> compression schemes though, and in the future we will likely
> implement a more flexible trajectory format that can contain mixes of
> trr/xtc/energy frames.
> Cheers,
> Erik
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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