[gmx-users] NPT equilibration with small cell

[Mark Abraham]

Hi,

The cut-offs are not free parameters. The quality of the model physics
depends on them (details are complex). Thus there is a minimum cell size
that is workable with typical force fields.

Mark

On Tue, 16 Feb 2016 19:02 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>