[gmx-users] sd integrator

Sai Pooja saipooja at gmail.com
Wed Sep 21 22:21:55 CEST 2011


The sd integrator is described in the manual as follows:
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?
Can such an integrator help in making trajectories less deterministic?


Quaerendo Invenietis-Seek and you shall discover.

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