Many thanks!
James
2014-06-09 19:39 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Mon, Jun 9, 2014 at 10:59 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
>
> > Jason,
> >
> > thanks for suggestions. Could you also tell me 1) may I use initial
> heating
> > of my system in NPT (not NVT) which could prevent such density
> fluctuations
> > during this stage using appropriate pressure coupling constant?
>
>
> Probably. Depends on the other settings. I typically heat over ~100 ps
> with restraints on the solute using NVT and then switch to NPT to stabilize
> the density. But I've also used NPT to heat before without adverse
> consequences. You should inspect your trajectory if you are unsure whether
> there are problems or not.
>
> However, heating with NPT will not lessen how much the unit cell will
> shrink. The only thing that it will help with is preventing the formation
> of bubbles if you see bubbles begin to form during your heating stage.
>
> 2) What
> > problems might be occurred during simulation in octahedral boxes?
> >
>
> Truncated octahedrons don't support anisotropic scaling (at least in
> Amber). However, it typically doesn't matter what shape periodic cell you
> use. [1]
>
> HTH,
> Jason
>
> [1] Except when it does matter, like for crystal simulations (that need to
> use the same shape box as the asymmetric unit cell) or instances where
> anisotropic pressure control is required, like for surfaces and layers
> (that typically require an orthorhombic box).
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Jun 09 2014 - 11:30:02 PDT
