[gmx-users] energy terms in following runs

[Ester Chiessi]

David van der Spoel wrote:

> 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?

No.

> 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).

In md0.log I read:bUncStart = FALSE

To prepare the second run, I used grompp giving in -c the last .gro file of the
first run.

Then, with tpbconv, I gave in -f the .trr file of the first run and the tpbconv
output told me that the last frame will be used.

Perhaps I shouldn't specify -c in grompp?

> >
> > 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
> > > >
> > > >
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
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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
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> > 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
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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