[gmx-users] -1.8 Equilibration pressure during MD simulation

[Mark Abraham]

Hi,

A time average over an equilibration run is not characteristic of the final
ensemble. Neither have you made a statistically significant observation of
the pressure, with an error estimate of 2.8... You have to run a long time
to do that. Instead think about the box volume or its density. Does that
value make sense?

Mark

On Wed, 10 May 2017 13:01 Dries Van Rompaey <dries.vanrompaey at gmail.com>
wrote:

> Hi,
>
> Pressure can often fluctuate wildly, especially in relatively small
> systems. You probably won't be able to achieve a stable pressure of 1 atm,
> and that's not a problem. As long as your pressure fluctuates around 1 atm
> you should be fine (you can use running average in xmgrace to check for
> this out). If it's not close enough yet, try extending your NPT
> equilibration until you are satisfied. The density is often a more stable
> indicator.
>
> Kind regards
>
> Dries
>
> On 10 May 2017 at 12:25, Quin K <profiles.ke at gmail.com> wrote:
>
> > Hi
> >
> > I used lyzozyme in water tutorial by virginia tech for MD simulation of a
> > protein, *pdb id = 2NT7*.
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
> > -tutorials/lysozyme/index.html
> > During equilibration step of MD simulation for a protein I got following
> > results for pressure.
> > Would the minus pressure value be a problem during MD production step?
> > What should be done to increase the pressure to 1 atm ?
> >
> >
> > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> > ------------------------------------------------------------
> > -------------------
> > Pressure                   -1.83425        2.8    124.812  -0.905452
> (bar)
> >
> >
> >
> > *Other results:*
> >
> > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> > ------------------------------------------------------------
> > -------------------
> > Density                     1025.74       0.32    2.01623    1.97406
> >  (kg/m^3)
> >
> >
> >
> > Thanks
> > Regards
> > --
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