[gmx-users] RE: Time step in md

Vitaly Chaban chaban at univer.kharkov.ua
Sat Sep 20 09:29:28 CEST 2008

> Hello,
> could you explain my the secret of choosing to time step for md
> integrator? I want to perform a 10-20 ns simulation in water in order
> to, for ex., calculate some interactions or to see if the structure
> would relax to a stable state. 
> If I use vsites, heavyh and LINCS I can run with 6 fs step. This would
> be quite quick. 
> I just wonder if this is `by book`. 
> I appreciate your help.

Hi Dimitry,

`by book` is when the error caused by discrete timestep is not significant
for your particular system. The standard timestep for water I believe
is 2 fs (or 1 fs is also popular). If you want using the bigger value I would suggest to perform
the single calculation with dt=2fs and the dt you want and compare the
basic system parameters.
It will determine if anything is wrong due to the timestep.

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
tel.: +38-097-8259698

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