[gmx-users] NPT equilibration with small cell
miguel.caro at aalto.fi
Tue Feb 16 23:19:55 CET 2016
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.
Dr. Miguel Caro
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
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
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.
On Tue, 16 Feb 2016 19:02 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
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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.
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.
More information about the gromacs.org_gmx-users