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

[Dries Van Rompaey]

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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