Dear David
Thank you for your reply. I guess I was worried about the momentum
transfer in the first part of my system due to stochastic nature of
Langevin thermostat. I will use the ntt=3 parameter for whole simulation
then.
Best
sam
On Sat, Jan 21, 2017 at 10:15 PM, David Case <david.case.rutgers.edu> wrote:
> On Fri, Jan 20, 2017, Samaneh Ghassabi Kondalaji wrote:
>
> > I would like to use Nose-Hoover chain (NHC) method for the first part of
> the
> > simulation where the water molecules are present and the langevin
> dynamics
> > after removal of (almost) all water molecules, to control the temperature
> > through the simulation.
>
> You can't do this in Amber, as far as I know. (There might be some
> undocumented trick...) But why do you want to do this? What is wrong with
> using the Langevin thermostat for all stages of the project?
>
> ....dac
>
>
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--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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Received on Mon Jan 23 2017 - 08:30:02 PST
