[gmx-users] Re: Re: RMSD in total energy

[Yujie Wu]

> Once again David!
> 
> So should I pay more attention to overall stabilization (=drift) of the total
> energy, energy components, and other properties such density than fluctuations
> in the total energy and just accept this disadvantage of the Berendsen
> temperature coupling (if Nose-Hoover isnt any better)? It is however quite
> often employed temperature coupling method and others should have had these
> "well-known" problems with "exact energy conservation" too?

The total energy here should be that of the extended system for NVT (or NPT)
simulations, because that is the quantity which should not drift in theory. The
Berendsen thermostat doesn't  corresponds to an extended system (and so the
total energy is doomed to drift), whereas the Nose-Hoover thermostat does. So if
you care about energy conservation, you should use Nose-Hoover thermostat for
your production runs.

That said, I am not sure whether the total energy from ener.edr file is for the
extended system or just for the simulation box (i.e., without the contribution
from the thermostat). Can any Gromacs guru comment on this?

Yujie


> 
> Thanks,
> 
> Janne
> 
> 
> > Janne Hirvi wrote:
> > > Hello David!
> > > 
> > > I use PME for Coulombic interactions (12Å) and Berendsen algorithms for
> > pressure
> > > and temperature couplings. Tutorial water example gives pretty much the
> > same
> > > bad fluctutational behaviour (with 500ps simulation using only 9Å cut-offs
> > for
> > > vdw- and Coulombic interactions). This same "problem" with approximately
> > same
> > > magnitude is in my water droplet simulations on surfaces (NVT), but I
> > thought
> > > that its connected to use vdw-cut-off and possibly to the Berendsen
> > temperature
> > > coupling (because these bulk simulations gave same fluctutational
> > behaviour)and
> > > has no crucial effects on simulations? 
> > 
> > Using Berendsen temperature coupling means that the fluctuation in 
> > temperature are not realistic, and hence those in the total energy.
> > You could try your luck with Nose-Hoover, although one probably needs an 
> > even fancier thermostat.
> > 
> > > 
> > > Janne
> > > 
> > > 
> > > Janne Hirvi wrote:
> > > 
> > >>Hello!
> > >>
> > >>I have made some rigid water simulations in NPT ensemble and now I am
> > > 
> > > wondering
> > > 
> > >>about the energy conservation. If I have understood right there will
> > always
> > > 
> > > be
> > > 
> > >>"small" drift when using cut-off for vdw-interactions (12Å), but how large
> > >>fluctuations it can introduce to the total energy? I think that the RMSD
> > in
> > > 
> > > the
> > > 
> > >>total energy should be much smaller than the RMSD in the potential or
> > kinetic
> > >>energy (ratio < 0.05), but however these fluctuations are now pretty much
> > >>equal.
> > > 
> > > How about Coulomb? Do you use PME?
> > > Which coupling algorithms do you use?
> > > 
> > > 
> > >>The situation is more or less the same for rigid water with time step of
> > 2fs
> > > 
> > > and
> > > 
> > >>for flexible water with 0.5fs, therefore long time step for rigid water
> > >>shouldnt be the problem. Should I be worried about the fluctuations or
> > just
> > > 
> > > pay
> > > 
> > >>attention to the drift?   
> > >>
> > >>
> > >>Thanks for any help or comments! 
> > >>
> > >>Janne
> > >>
> > >>
> > > 
> > >
> >
> ------------------------------------------------------------------------------
> > > 
> > >>Janne Hirvi, MSc(Physical Chemistry), Researcher
> > >>University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu,
> > FI
> > >>Tel: +358 13 2514544 & +358 50 3474223
> > >>E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
> > >>
> > > 
> > >
> >
> ------------------------------------------------------------------------------
> > > 
> > > 
> > 
> > 
> > -- 
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > 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
> 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.