[gmx-users] NPT equilibration with small cell

[André Farias de Moura]

maybe just a historical curiosity, but small systems with only 100
molecules or so and cutoffs of 0.7 nm were considered as best practices,
maybe even state-of-art, in computer simulations of liquids:

J. Chem. Phys. 79, 926 (1983); http://dx.doi.org/10.1063/1.445869

nowadays you have to use systems like those for your AIMD for the same
reasons they had too back in the day: not enough computer power to treat
the system of the size you would like to.

so I would do just like Vitaly suggested: classical MD with small
system/small cutoffs, DFT geometry optimization and then your goal, the
AIMD simulation.

Andre

On Wed, Feb 17, 2016 at 9:44 AM, VITALY V. CHABAN <vvchaban at gmail.com>
wrote:

> you are on the right way.
>
> set high pressure.
>
> set cut-offs to half box side.
>
> run classical MD, ~10 000 steps, and, afterwards, manually increase the box
> sides to mimic the experimental density
>
> in the plane-wave DFT, run local optimization prior to AIMD.
>
>
>
>
>
>
>
>
> On Tue, Feb 16, 2016 at 4:01 PM, Miguel Caro <miguel.caro at aalto.fi> wrote:
>
> > Hello,
> >
> > I was wondering if there is any reason why one should expect a constant
> > pressure simulation not to work for a small cell. I am running a very
> small
> > cell (1.2 nm^3) simulation because I need it as input for ab initio MD. I
> > am trying to simulate NPT at 1 atm and it seems like my cell, a mixture
> of
> > water and methanol, is expanding uncontrollably (to 10 nm^3).
> >
> > Is it not possible to do NPT for cells this small? I should add that NVT
> > seems to work just fine for the same system.
> >
> > These are the settings I am using for the pressure coupling:
> >
> > Pcoupl = MTTK
> > tau_p = 0.2
> > compressibility = 4.5e-5
> > ref_p = 1.0
> >
> > I have tried to do the same simulation with a supercell made up of 2x2x2
> > periodic copies of my small cell and that seems to work fine. For that
> > simulation, the only difference besides the cell size was the neighbors
> > cutoffs, which I could increase from rlist = rcoulomb = 0.45, rvdw = 0.5
> > for the small cell to rlist = rcoulomb = 0.8, rvdw = 1.1 for the
> supercell.
> > For the small cell the cutoff radii are rather limited by the box size.
> >
> > Thanks in advance,
> > Miguel
> >
> > --
> > *Dr. Miguel Caro*
> > /Postdoctoral researcher/
> > Department of Electrical Engineering and Automation,
> > and COMP Centre of Excellence in Computational Nanoscience
> > Aalto University, Finland
> > Personal email: *mcaroba at gmail.com*
> > Work: *miguel.caro at aalto.fi*
> > Website: http://mcaroba.dyndns.org
> > --
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090