[gmx-developers] Re: printing to edr in source code

[Inon Sharony]

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).

            Inon.

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
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
> Please consider your environmental responsibility before printing 
> this e-mail.

-- 
Inon   Sharony
ינון     שרוני
+972(3)6407634
atto.TAU.ac.IL/~inonshar
Please consider your environmental responsibility before printing this e-mail.
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