[gmx-users] sd integrator

Mark Abraham Mark.Abraham at anu.edu.au
Thu Sep 22 01:40:42 CEST 2011

On 22/09/2011 6:21 AM, Sai Pooja wrote:
> Hi,
> The sd integrator is described in the manual as follows:
> sd
> An accurate leap-frog stochastic dynamics integrator. Four Gaussian
> random number are required per integration step per degree of freedom.
> With constraints, coordinates needs to be constrained twice per
> integration step. Depending on the computational cost of the force
> calculation, this can take a significant part of the simulation time.
> The temperature for one or more groups of atoms (tc_grps) is set with
> ref_t [K], the inverse friction constant for each group is set with
> tau_t [ps]. The parameter tcoupl is ignored. The random generator is
> initialized with ld_seed. When used as a thermostat, an appropriate
> value for tau_t is 2 ps, since this results in a friction that is
> lower than the internal friction of water, while it is high enough to
> remove excess heat (unless cut-off or reaction-field electrostatics is
> used). NOTE: temperature deviations decay twice as fast as with a
> Berendsen thermostat with the same tau_t.
> It is not clear what is the purpose of this integrator and how is it
> different from ld. Can someone refer me to a paper?

See manual section 3.8 and ref therein.

> Can such an integrator help in making trajectories less deterministic?

It's still going to be deterministic, because the RNG is.


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