Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat

From: James Starlight <>
Date: Thu, 4 Jul 2019 10:05:38 +0200

Thank you so much, David!
and normally which tautp would be generally better when ntt=1
(berendsen coupling) ?
as I have understood correctly, bigger values e.g. tautp=1.0 introduce
bias of the thermostat on the dynamics of the system, doesn't it?

Yours with thanks,


ср, 3 июл. 2019 г. в 19:34, David Case <>:
> On Wed, Jul 03, 2019, James Starlight wrote:
> >And normally gamma_ln=5.0 (more virtual collisions) is better for the
> >equilibration of the flexible systems (to damp the dynamics of loops )
> >while gamma_ln=2.0 is for the subsequent production run, doesn't it ?
> In my experience, there is not much difference when setting gamma_ln in
> the range of 1 to 5. You could experiment to see if you see anything on
> your system.
> ....dac

AMBER mailing list
Received on Thu Jul 04 2019 - 01:30:05 PDT
Custom Search