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

Shreyas Kaptan shreyaskaptan at gmail.com
Sat Jun 2 08:17:58 CEST 2018

The cavity, which is due to negative pressure in the system, might imply
one of the two things:

The Box is too big for the system or that the MD simulation implodes the
system somehow. I have seen issues like these when the system is not well
minimized and has some obvious artefacts like "broken" bonds or missing
atoms in the structure and in topology.

But if it is none of the above, I would try a smaller timestep if possible.
Maybe it is a bad clash that somehow generates a negative pressure in the
system (although I do not profess to know how).

On Sat, Jun 2, 2018 at 6:28 AM Alex <nedomacho at gmail.com> wrote:

> 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
> rejoice.
> Alex
> 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
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Shreyas Sanjay Kaptan

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