[gmx-developers] Re: printing to edr in source code
InonShar at TAU.ac.IL
Tue Sep 8 20:14:55 CEST 2009
Thanks for the reply, Berk.
So, it is as I suspected. But whatabout the potential energy? using the positions from the .trr file(extracted using g_traj) the potential energy I get is not exactly thesame as that given by the .edr file (via g_energy).
Quoting "Inon Sharony" <InonShar at TAU.ac.IL>:
> Hi GMX developers!
> (note: if this seems too rudimentary -- I posted first on the users'
> list but no one picked up the glove...)
> I'm trying to check that the energies I can calculate using the
> trajectory output are the same as those given by g_energy. I'm
> running a diatomic for only a couple of steps and already there are
> inconsistencies. I'm using g_traj to print out the x's and v's from
> the .trr file (indouble precision). The steps I'm looking at are at
> the beginningof the trajectory, but since my initial conditions are
> zero velocitiesand configuration very close to the energy-minimized
> one, I don't thinkthere should be any excessively large forces (the
> total energy is about21 kJ/mole).
> I suspect that one possible factor could be that the leap-frog
> algorithm uses trajectory data (i.e. positions and velocities)
> different from those printed to the trajectory file. For example, it
> appears that the velocity printed out in the .trr file is notstrictly
> the velocity at that time-step, but the velocity given by anaverage
> of the kinetic energies half a time-step forwards and back(since GMX
> uses the leap-frog algorithm). This has managed to explainthe
> discrepancy in the kinetic energies (the one given by g_energy andthe
> one calculated from v's given by g_traj). As for the potentialenergy,
> I'm still trying to figure that out...
> Could you please direct me to the file and line in the source code
> where the kinetic and potential energies are calculated, just before
> they are printed to the edr file?
> Thanks very much in advance,
> Inon Sharony
> ינון שרוני
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