[gmx-developers] suggestion: velocities.xtc

Erik Lindahl lindahl at cbr.su.se
Tue Oct 17 09:25:13 CEST 2006


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.



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