[gmx-users] NPT equilibration with small cell

[Caro Miguel]

Dear Mark,

Thanks for your answer. I will try to learn more about how the cutoffs affect the simulation results. Is there any reading besides the manual that you could recommend on this topic? I would particularly appreciate anything on how to handle small cell simulations.

Thanks again,
Miguel

--
Dr. Miguel Caro
Postdoctoral researcher
Department of Electrical Engineering and Automation, and
COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Email: mcaroba at gmail.com
Work: miguel.caro at aalto.fi
Website: http://mcaroba.dyndns.org
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abraham at gmail.com]
Sent: 16 February 2016 20:06
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] NPT equilibration with small cell

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
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