[gmx-users] energy terms in following runs

[Ester Chiessi]

Thanks for all your suggestions.

My last question now is:

Is it more correct to generate velocities again, when you want to increase
the time step after a history of previous runs?

Or to mantain the last velocities can have any sense?

Anton Feenstra wrote:

> David van der Spoel wrote:
> > On Fri, 2003-02-21 at 14:52, Ester Chiessi wrote:
> [..]
> >>
> >>Pheraps this happened because I changed the time step?
> [...]
> > If you change the time step the kinetic energy will be discontinuous.
>
> Worse: your velocities will be wrong; they are from the 'half' timestep
> in the Leapfrog algorithm, but if you change timestep, the 'location'
> of the half timestep will have shifted... It should be possible to
> correct for that, perhaps by taking an appropriately weighted average
> between velocities at last step and one-but-last, but usually you
> do not write .trr every md step.
>
> --
> Groetjes,
>
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
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--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
       39*6*72594874
Fax:39*6*72594328