[gmx-users] Settings of SD integrator
johnwhittake at zedat.fu-berlin.de
Mon Apr 1 14:48:09 CEST 2019
> For these simulations, the papers suggest the SD integrator.
> But mdp options for SD integrator is not defined clearly
> I've included ld_seed
> tried changing the tau_t
> Could anyone tell me what correct mdp options are required to be changed
> while using SD integrator?
Have you tried running simulations with these mdp settings that you
changed? What simulation parameters are used in the paper?
- ld_seed is simply a value that determines the random noise term in the
equation of motion. I normally just set this to -1 (its default value)
because this generates a pseudorandom number, but you can set it to
whatever you want.
The mdp options you have to change to use SD are just the ones you listed,
plus ref_t which you must have been using for your equilibration.
So, setting ld_seed, tau_t, and ref_t should be all you need to do to use SD.
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