[gmx-users] NPT equilibration with small cell
jalemkul at vt.edu
Wed Feb 17 01:32:58 CET 2016
On 2/16/16 5:19 PM, Caro Miguel wrote:
> 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.
Start with the source of your force field parameters. The nonbonded setup is
essentially a fixed element of the force field; alterations change the balance
of forces and may even invalidate the findings completely depending on how badly
you mess with them.
Those cutoffs determine the minimum size of the system, as one must avoid
minimum image violations. So there is a lower limit on the size of the system.
Using MTTK as a barostat will likely allow for rather large fluctuations in
pressure and subsequently the unit cell, so it may not be a very good choice for
a small system.
If you're trying to prepare some small system for further study, it may be wise
to run your simulation on a larger system and then carve out part of it for the
ab initio MD. It may simply not be practical or possible to run a tiny system
with convention MD, given the inherent size requirements.
> 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
> 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, 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
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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