[gmx-developers] Why is not the thermostat used in the first step?

hessb at mpip-mainz.mpg.de hessb at mpip-mainz.mpg.de
Sat Jun 4 11:56:47 CEST 2005

Quoting ramon at juguete.quim.ucm.es:

> Hello,
> I see that in the first step the thermostat is not used.

This has been changed in the CVS code.

> This is a problem when one wants to equilibrate a system where
> molecules overlap. Using a Berendsen thermostat with a time constant
> of timestep/10 would allow to remove overlaps for these systems.

This would not help as v(dt/2) is scaled with T(-dt/2) which
has no meaning at the start of a run. T(-dt/2) is just given
by the input velocities.


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