[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
>lookout for?
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
secondary structure.

>Lieven Buts
>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.

Groeten, David.
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 mailing list