[gmx-developers] [gmx-users] Wrong Nose-Hoover integrator

Michael Shirts mrshirts at gmail.com
Wed Mar 30 16:35:23 CEST 2005

Hi, all-

> Currently I am having a long discussion with Michel Cuendet.
> I have figured out that for the coupling we should use the temperature
> at t-1/2 and then we can have proper, reversible leap-frog Nose-Hoover
> integration,
> I already have this working, so this can make it into 3.3 (see the link to
> Michel Cuendet original post for the algorithm and reference).
> There are even better, symplectic, integrators, but we can consider this
> later.
> Proper NPT with constraints is much more complicated and might require
> velocity verlet with iteration of  constraint calculations.
> This will probably have to wait till after release.

Symplectic is better when at all possible, but this sounds like a good
solution in the meantime, and anything else can almost certainly wait
until after release.  I'm very willing and eager to help with this.

For the iteration of contstraints -- If you look at Anderson's
original RATTLE paper it uses an approximation for the full step
volume velocity in the intermediate steps ends up working extremely
well -- conserving enthalpy pretty much down to machine precision,
meaning constraints only have to be evaluated once (at least usually!)
 We can discuss this later.


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