[gmx-users] sd integrator

Mark Abraham Mark.Abraham at anu.edu.au
Thu Sep 22 02:09:14 CEST 2011

On 22/09/2011 9:57 AM, Sai Pooja wrote:
> But is the effect of varying ld_seed.. can that make different
> trajectories stochastic?

Any single MD or SD trajectory is literally stochastic. Either can start 
from the same point with respectively different ld_seed or gen_seed and 


> 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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