[gmx-users] Is it still not possible trjorder to print out velocities and forces in trr trajectories? It would be really useful..

Mark Abraham mark.j.abraham at gmail.com
Tue Nov 15 13:35:46 CET 2016


Yes, probably useful, but unfortunately nobody has wanted to implement it
before now.

You can of course use gmx select to write out a dynamic per-frame selection
of waters, and then gmx trjconv to extract frames that include velocities.
That's not very efficient, but does what you seem to want.


On Tue, Nov 15, 2016 at 12:16 PM Juan José Galano Frutos <juanjogf at gmail.com>

> Hi there:
> I am trying to analyze a water shell around a protein, and we are studing
> for instance deltaH in some molecular processes. In this sense as you know
> Enthalpies not only depend on Potential energy but also on Kinetic energies
> and a term pV, so that it is crutial having velocities for calculating
> Kinetic energies. As far as I know the only tool exists to order and
> extract by for instance a distance criterium a water shell around a protein
> is TRJORDER, however this program not print out the velocities in the
> output trajectories so it is impossible to obtain the Enthalpies in my
> anallysis.
> Could you suggest to me any solutions...
> Wouldn't be useful to add that functionality to TRJORDER program? Would it
> be?
> Thank you very much in advance.
> Juan José Galano Frutos
> Department of Biochemistry and
> Molecular and Cellular Biology,
> Faculty of Sciences,
> University of Zaragoza
> Pedro Cerbuna # 12, 50009
> Zaragoza (Spain)
> +34 976 76 28 06 <+34%20976%2076%2028%2006>
> Institute for Biocomputation and
> Physics of Complex Systems (BIFI)
> Mariano Esquillor, Edificio I + D - 50018
> Zaragoza (Spain)
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