[gmx-users] Timestep and force field

[Jussi Lehtola]

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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.
-- 
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Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50632
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Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi
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