[gmx-users] Re: RMSD in total energy

Janne Hirvi janne.hirvi at joensuu.fi
Sat Jan 14 13:02:52 CET 2006

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? 


Janne Hirvi wrote:
> Hello!
> I have made some rigid water simulations in NPT ensemble and now I am
> about the energy conservation. If I have understood right there will always
> "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
> 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
> 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
> 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 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

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