[gmx-users] Timestep and force field

Jussi Lehtola jussi.lehtola at helsinki.fi
Sun Mar 22 10:28:02 CET 2009

Varsha: have you subscribed to the list yet? Please do so if you

On Sun, 2009-03-22 at 13:18 +0400, varsha gautham wrote:
> 3. hen how to choose a timestep for a simulation like a picosecond or
> a nanosecond?What is a timestep?
> I have gone through many materials and stuffs related to Gromacs.But i
> dint get a clear idea, addressing this 2 questions.I will be really
> thankful if someone took time to read to this mail patiently and reply
> me with a solution which am looking for months together.Thanks in
> advance.

The time step is the step used in integrating the equations of motion (F
= ma). The algorithm used to integrate the equations is leap-frog, which
you can look up in the manual (eqns 3.20 and 3.21).

The timestep in GROMACS is usually of the order of femtoseconds (1 fs =
0.001 GROMACS internal units). To determine what time step to use for
your system turn off all pressure and temperature couplings (NVE
ensemble) and run a few short simulations with different time steps.
Look at the potential, kinetic and total energy output of the runs: if
the total energy stays constant the time step is sufficiently small.
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50632
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi

More information about the gromacs.org_gmx-users mailing list