Ming, if you want to study dynamic properties of a fluid you shouldn't use
any thermostat since they all have an affect the velocities of the
particles.
If you want to study a system at a certain temperature then sample
different total system energies that are properly representative of the
canonical ensemble.
e.g. Run a # NVE systems with different energies where the energies are
sampled from the canonical ensemble (NVT). A simple way of doing this is
run a system for a long time at NVT and then pick a # of
configurations/frames from it to be the starting configurations for your
NVE runs.
The # should be as many as you can do (better sampling) and the starting
frames should be taken from separate times that are farther away from each
other than the time correlation of the system energy.
Tom
On Thu, Feb 22, 2018 at 6:22 AM, Ming Tang <m21.tang.qut.edu.au> wrote:
> Dear experts,
>
> I want to study the viscosity of a protein in water using amber. Based on
> the literature, the Lowe-Anderson thermostat provides more accurate
> viscosity than the Langevin thermostat in NAMD. I found that AMBER does not
> have the Lowe-Anderson thermostat, but has Anderson thermostat. NAMD is not
> available to me. May I ask which thermostat in AMBER gives a better
> characterization of the viscosity?
>
> Thanks very much,
>
> Ming
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>
--
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Tom Kurtzman, Ph.D.
Associate Professor
Department of Chemistry
Lehman College, CUNY
250 Bedford Park Blvd. West
Bronx, New York 10468
718-960-8832
http://www.lehman.edu/faculty/tkurtzman/
<http://www.lehman.edu/faculty/tkurtzman/index.html>
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Received on Thu Feb 22 2018 - 05:00:02 PST
