[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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