[gmx-users] NPT Equilibrium?

[Johnny Lu]

No protein md is truly at equilibrium?
http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b


On Fri, Oct 3, 2014 at 1:42 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Johnny,
>
> Equilibrium in energy, maybe, but check individual energy components,
> rather than totals. Equilibrium in dynamics is for sure not reached yet.
>
> Cheers,
>
> Tsjerk
> On Oct 2, 2014 7:52 PM, "Johnny Lu" <johnny.lu128 at gmail.com> wrote:
>
> > Hi.
> >
> > The system is a ~ 165 amino acid protein with a 7 amino acid substrate,
> in
> > an about 9000 water rhombic dodecahedron water box.
> >
> > I used thermostat for the whole system.
> >
> > 1. minimization to force < 100.
> > 2. NVT with position restrain on protein 0.3 ns
> > 3. NPT with position restrain on protein
> > 4. 30 ns NPT without position restraint.
> >         Average Total Energy: -310151
> >         Total-Drift: -98.7985
> > 5. 0.06 ns NPT
> >         Average Total Energy: -310371
> >         Total-Drift: 618.659
> > 6. 59 ns NPT
> >         Average Total Energy: -310207
> >         Total-Drift: 24.0559
> > 7. 59.1 ns NPT
> >         Average Total Energy: -310204
> >         Total-Drift: 25.1117
> > 8. 30 ns NPT
> >         Average Total Energy: -310204
> >         Total-Drift: -31.0966
> >
> > 9. 30 ns NPT
> >         Average Total Energy: -310210
> >         Total-Drift: -29.4525
> >         Average Pressure: 1.16985
> >         Total-Drift: -0.0824936
> >
> > Is this at equilibrium yet? The barostat set to 1 bar.
> > --
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