[gmx-users] sd integrator

Sai Pooja saipooja at gmail.com
Thu Sep 22 01:57:06 CEST 2011

But is the effect of varying ld_seed.. can that make different
trajectories stochastic?

On Wed, Sep 21, 2011 at 7:40 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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.
> Mark
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