[gmx-users] energy terms in following runs

[Ester Chiessi]

Thanks for your answer.

I verified ( with g_energy ) that there are small differences ( ranging from
about 0.3 to 1 percent ) in every energy terms, except Coulomb(1-4).
The bond term is different, too; I'm using SHAKE to fix distances only for
hydrogen atoms.

David wrote:

> On Tue, 2003-02-18 at 16:06, Ester Chiessi wrote:
> > Dear all,
> >
> > I performed two following md runs ( 1000 + 1000 steps = run a + run b ) by
> > using tpbconv to restart the second run (a) from the last frame of the
> > first run (b).
> > I was surprised to found the energy terms calculated for the last
> > structure of run (a) were different ( in some cases of some percent ) from
> > the corresponding values of the first structure of run (b).
> >
> > I'm trying to obtain the equilibration for my system. Is it incorrect to
> > proceed by following dynamics steps?
>
> This is fine. Have you investigated (using g_energy) what the difference
> in the energy file comes from??
>
> >
> > Thanks
> >
> > Ester
> >
> >
> > --
> > 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
> >
> >
> > _______________________________________________
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> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel,        Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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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