[gmx-users] NPT equilibration with small cell
VITALY V. CHABAN
vvchaban at gmail.com
Wed Feb 17 12:45:23 CET 2016
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:
> 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,
> *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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