[gmx-users] RMSD in total energy

Janne Hirvi janne.hirvi at joensuu.fi
Sat Jan 14 10:24:18 CET 2006


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

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 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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