[gmx-users] fit

[Nguyen Hoang Phuong]

> Nguyen Hoang Phuong wrote:
> >
> > Dear All,
> >
> > I used trjcov_d to fit the structures of the simulated trajectory to the
> > reference structure in the structure file. Then I use g_energy_d to
> > display the kinetic energy of both original trajectory and fitted one. It
> > is suprise because the results are difference. I thought that the fit
> > function only do fit for the coordinates, not for the velocity. Can anyone
> > give an explanation. Thanks in advance.
>
> It is even more surprising to me: trjconv reads & writes trajectories
> (in your case, probably .trr) while g_energy reads energy files (.edr).
> So there is no way trjconv can possible change your energies...
>
> But you are right that fitting in trjconv does not affect velocities.

I mean that I used rerun program to get the energy from the fitted
trajectory (rerun.edr) and compare with those from original one (run.edr).

>
>
> --
> Groetjes,
>
> Anton
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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