Without a thermostat, can AMBER acheive sufficient precision to avoid the
build up of thermal energy in regions where integration energy are largest
(typically the solvent if the water is rigid), or other flying ice cube
type problems? Using velocity Langevin as a thermostat has its own problems
with dynamics, but at least it guarantees the correct distribution of
kinetic energy across all particles. I guess I'm just not convinced that
NVE is without its own set of problems.
On Thu, Feb 22, 2018 at 5:52 AM, Tom Kurtzman <simpleliquid.gmail.com>
wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ************************************************
> 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 Fri Feb 23 2018 - 15:30:02 PST
