[gmx-users] RMSD in total energy

[David van der Spoel]

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
> ------------------------------------------------------------------------------
> 
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-- 
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
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