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

[Janne Hirvi]

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?

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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++