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

[Juan José Galano Frutos]

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

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)