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

Alex alexanderwien2k at gmail.com
Sat Jun 2 06:21:39 CEST 2018

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,

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