[gmx-users] Atoms get frozen with "Nose Hoover thermostat with Parrinello-Rahman barostat" for a system of an ion of charge +2 in flexible water molecules

[ms]

On 27/06/12 05:20, Surya Prakash Tiwari wrote:
> Dear Gromacs users,
>
> I am having a very strange problem with "Nose Hoover thermostat with
> Parrinello-Rahman barostat" NPT simulations for a system of an ion of
> charge +2 in flexible water molecules. Flexible water is taken from J.
> Chem. Phys. 124, 024503 (2006); http://dx.doi.org/10.1063/1.2136877.
> The ion is [UO2]2+ with charge on U=2.5 and each O has -0.25.
>
> Atoms very soon get frozen after the simulation starts and they remain
> frozen, they do not move at all. Only simulation box oscillates, which
> causes atoms to oscillate little bit but they do not move at all.

To me it looks like a case of this artefact:

http://en.wikipedia.org/wiki/Flying_ice_cube

but I don't know exactly what is causing it in your system. Perhaps the 
article can help you triage...

-- 
Massimo Sandal, Ph.D.
http://devicerandom.org