[gmx-users] energy terms in following runs

[David van der Spoel]

On Wed, 2003-02-19 at 14:42, Ester Chiessi wrote:
> 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.
Are you using xtc? In that case energies will be different due to
roundoff in the coordinates. Otherwise you should doublecheck that
unconstrained start is on (in md.log)
and that you are not generating velocities (but tpbconv does not do
this). 
> 
> 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
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. 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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