[gmx-users] Cavity in the system after NVT equilibration

Alex nedomacho at gmail.com
Sat Jun 2 06:28:34 CEST 2018

Equilibration under NVT is a very bizarre approach, I am not even going 
to ask why you're doing this.

I am known for perverse use of Gromacs, but please follow EM > NPT 
equilibration (Berendsen thermostat, etc) > production.

The fact that you don't see the cavity at high temperature is that you 
have overheated gas under high pressure. The fact that annealing it down 
brings back the cavity means that the physics works and everyone should 


On 6/1/2018 10:21 PM, Alex wrote:
> Dear all,
> I have a system containing 4000 water molecules+700 of molecule A + 300 of
> molecule B. After minimization, the system undergoes a 2ns NVT equalization
> at 298.15 K which gives a big cavity in the system at the end, whereas the
> cavity does not show up at 650 K equlibration. But what I need is the
> system at 298.15 K. So, I tried to rampe down the temperature from fully
> equilibrated system at 650 to 298.15 by the step of 35 K (in total 10 ns)
> hoping to solve the problem by cooling down the system from the temperature
> at which the system is normal to the desired temperature, but at the end
> the cavity appears  unfortunately.
> So, I wonder how I should equilibrate the system in order to avoid having
> the cavity?
> Thank you,
> Alex

More information about the gromacs.org_gmx-users mailing list