[gmx-users] on the ussage of SD1 integrator

Berk Hess gmx3 at hotmail.com
Wed Feb 13 15:57:34 CET 2013


With tau_t=2 the sd1 integrator should be ok.
But in 4.6.1, which will be released this week, the performance issues with the sd integrator are fixed.



> Date: Wed, 13 Feb 2013 09:19:46 +0300
> From: jmsstarlight at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] on the ussage of SD1 integrator
> Dear Gromacs users!
> Commonly I'm using langevin's dynamics for  thermostat modelling in my
> simulations of the membrane proteins
> (sd integrator without t_coupl with tau_t=2.0)
> Recently I've found that with sd1 integrator I can obtain better
> performance ( up to 50% in comparison to sd integrator). Could I use
> that integrator for modelling of stochastic thermostat with the same
> tau_t which I've used with SD ?
> Also during ussage of that thermostat I obtain notions from grommp like
> NOTE 4 [file ./mdps_cuda/md_sd.mdp]:
>   With constraints integrator sd1 is less accurate, consider using sd
>   instead
> What should I do to reduce such degree of inacuracy of SD1?
> Thanks for help,
> James
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