[gmx-users] Unreasonably high pressure values

Mark Abraham mark.j.abraham at gmail.com
Mon May 15 18:36:11 CEST 2017


Convergence times depend on system type and size, of course, but an
equilibration on an inhomogeneous system should probably run for more than
a few nanoseconds. That might help expose whether the issue is the system,
or the protocol, or the applied force.


On Mon, 15 May 2017 18:25 Kamps, M. <m.kamps at student.rug.nl> wrote:

> Dear GMX users,
> I am struggling with understanding my systems behaviour.
> I have a semi-isotropic system where my bottom and upper plane are
> composed of gold FCC plates. In between is a fluid, which during
> equilibration is stationary (no acceleration). I equilibrate the
> system with a Berendsen barostat, as the literature suggests. The
> compressibility is that of the fluid used (Hexadecane C16H34), while
> the reference pressure is 1 bar. See the below section of my systems
> MDP:
> ; Pressure coupling is on
> pcoupl                    = berendsen        ; Pressure coupling on
> pcoupltype                = semiisotropic            ; uniform scaling
> of box vectors
> tau_p                    = 2.0                ; time constant, in ps
> ref_p                    = 1.0     1.0            ; reference pressure, in
> bar
> compressibility             = 0      8.6e-5            ; isothermal
> compressibility, bar^-1
> When I equilibrate the system, everything appears to be normal. The
> volume shrinks a little to compress the fluid, which leads to a
> correct density (correct as in corresponding with known values of the
> real-life density). The fluid behaves as expected and everything looks
> good.
> I then want to use the system to accelerate the fluid, however that
> blows up the system. Blowing up as in; fluctuations in the box size,
> shrink, expand, rapid shrink, rapid expand, extreme shrink, blowing
> up.
> Upon inspection, during equilibrating the pressure of my system nicely
> converges, however, it converges to -6000 bar, which seems rather
> strange.. How does this happen? What am I doing wrong?
> I use a 0.5 fs timestep, equilibriate over 400.000 steps (0.2 ns),
> 300K v-rescale temperature coupling, PME electrostatic calculations.
> Kind regards,
> Mark
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