Depending on the properties you are interested in will determine your
thermostat. Both the Andersen and the Langevin thermostats sample canonical
distributions, so either will give correct structural configurations and
thermodynamic properties. However, time-dependent properties (such as
diffusion) are not correct, because the thermostats are stochastic and
include random fictitious collisions. If you are interested in transport
properties, such as diffusion coefficients, then a deterministic thermostat,
such as the Nose-Hoover, is recommended.
Hope this helps.
-----Original Message-----
From: Karolina Mitusińska (Markowska) [mailto:markowska.kar.gmail.com]
Sent: Tuesday, November 22, 2016 2:31 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] DIfferences between thermostats
Dear Amber Users,
I would like to analyse a flow of water molecules through a protein. The
problem is, I'm not sure which thermostat to choose to have the _correct_
behaviour of water molecules. For example if my system have two tunnels and
one is more hydrophobic than the secnd one - which thermostat should I
choose?
Sorry for such stupid question. I've spend whole day reading papers about
different thermostats and yet I only know that there could be some
differences in water molecules behaviour, but I still don't understand the
reason of these differences.
Could you help me, please?
Best regards.
Karolina Mitusińska
PhD student
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Received on Tue Nov 22 2016 - 12:00:05 PST
