[gmx-users] fit

[Anton Feenstra]

Nguyen Hoang Phuong wrote:
> 
[...]
> > 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).

OK, that makes sense. It seems likely that rounding of the coordinates,
due to the fitting, can give you energy changes, but it still shouldn't
affect velocities. However, I don't know how mdrun -rerun affects
velocities; it could be that constraints are applied, or temperature
coupling. I've never tried this... ;-) See if you still have differences
with constraints and tcoupl turned off.


-- 
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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