Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Fri, 9 Jul 2010 22:58:16 -0700

> > As the manual script shows, constant V equ is essential to place the adding
> > solvate to reasonable positions and regulate the temperature at the same
> > time. I have make a trail to directly heat the system after minimization
> > with constant pressure, but this work failed for some atoms with unlimited
> > rate (*****). I assume the heat precedure makes the system unstable when it
> > go along with constant pressure.
> In this case one needs to warm slowly, then it should be ok.

I should add that this method, while it can get the system warmed
to 300K successfully, no longer seems to be the consensus. My
impression of the consensus is that one warms NVT with cartesian
restraints, which allows the artificial water and ion placement
to relax in a low-density regime, then one switches to NPT to
equilibrate density, perhaps removing restraints in the process.
(With NPT, restraints should be scaled with the system, is this done?)
I think this equilibration more methodically solves the equilibration
problem than warming with NPT.


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Received on Fri Jul 09 2010 - 23:00:04 PDT
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