[gmx-users] Simulation timestep: how to assess?
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jul 23 09:50:32 CEST 2002
On Mon, 22 Jul 2002, Lieven Buts wrote:
> 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?
This is not trivial... I am doing some testing on this stuff now, and long
timesteps combined with dummies give me unfolding proteins while without
dummies and 2 fs the systems are stable. These are long-time effects (i.e.
after a couple of ns things start to happen). I have to do more test
before I can conclude anything.
> 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
Same answer, but you need some experimental observations to test. RMSD is
the simplest but every little thing could help. An important test is the
>Vrije Universiteit Brussel
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users