[gmx-users] NPT Equilibrium?

[Tsjerk Wassenaar]

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.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>