[gmx-users] fit

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
 _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "Check Your Input" (D. Van Der Spoel)                 |
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