[gmx-users] tpbconv for following runs

[Ester Chiessi]

Really thanks, Anton, for this explanation!

Ester


Anton Feenstra wrote:

> Ester Chiessi wrote:
> > Hi all,
> >
> > I'm using tpbconv to produce an MD calculation by following runs.
> [...]
>
> > I expected that all terms were identical, not only the potential energy
> > contributions.
> >
> > May I consider negligible these discrepances?
>
> Yes. Although this has been discussed at some length already a few times,
> it is not a bad thing to explain it once again.
>
> In the verlet/leapfrog integration scheme (for MD), coordinates are
> available at the whole timestep (t, t+dt, and so on), and velocities
> at the half (t-dt/2, t+dt/2, t+(3/2)dt, and so on). In one 'x+v' frame
> in the .trr file you will find coordinates at 't' and velocities only
> at 't+dt'. However, the correct velocities for calculating physical
> properties (kinetic energy, temperature, pressure) should be taken
> at the whole timestep. Normally during your simulation this is achieved
> by taking the average of the previous (t-dt/2) and current (t+dt/2)
> velocities. In the .trr file, however, the previous velocities are not
> present. This causes the observed discrepancies, and will cause the
> continuation simulation to be *not* the exact same as an un-interrupted
> simulation would have produced. The actuall error made, however, is
> very small and both simulations (interrupt+continued and uninterrupted)
> can be considered 'correct'.
>
> --
> 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/       |
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> |_____________|_______________________________________________________|
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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