[gmx-users] Simulation timestep: how to assess?

Lieven Buts lieven at ultr.vub.ac.be
Mon Jul 22 10:56:07 CEST 2002

  I have run simulations of a system (one protein molecule and
8 Na+ ions in SPC water) using timesteps of 2 and 4 fs. In both
cases the temperature, density and total energy, as well as the
box volume and the RMSD of the protein with respect to the starting
structure are stable. The temperature, density, volume and RMSD
oscillate in the same ranges for both timesteps. The total energy
fluctuates between -5.75e5 and -5.77e5 kJ/mol for the 2 fs timestep,
and between -5.70e5 and -5.73e5 kJ/mol for the 4 fs timestep. The RMSD
also seems to be a little bit higher for the longer timestep (0.13 on
average instead of 0.10 nm). Is this sufficient to draw conclusions
about the acceptability of a 4 fs timestep?

  More generally, what should one look for in determining the optimal
timestep for a simulation? Do you just have to make sure that the system
does not explode, or are there more subtle artefacts to be on the
lookout for?

Lieven Buts
Vrije Universiteit Brussel

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