AMBER Archive (2009)

Subject: Re: [AMBER] explicit solvent NMR refinement

From: case (case_at_biomaps.rutgers.edu)
Date: Sun Jun 28 2009 - 08:19:11 CDT

On Sun, Jun 28, 2009, Sally Pias wrote:
>
> I am following a protocol for explicit solvent refinement of NMR
> structures described by Xia, et al. (J Biomol NMR, 22: 317–311, 2002).
> The protocol uses Berendson temperature control throughout, with a
> heat bath coupling constant of 1.0 ps. My understanding from reading
> Amber Reflector Archive discussions is that Langevin temperature
> control is now preferred in general, particularly when one is
> interested in dynamics. Does this preference apply to NMR refinement,
> where it is not really dynamics that one is after?

All thermostats disrupt dynamics, Langevin more so in general than Berendsen.
But the real advantage of the Berendsen thermostat for simulated annealing is
that you can easily control the rate of heating or cooling. A Langevin
thermostat moves the system very quickly to the target temperature. So, I
don't think you need to replace the Berendsen idea in this context.

...dac

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber