[gmx-users] NPT equilibration with small cell

[Miguel Caro]

Dear Justin,

Thanks for your very helpful answer.

Miguel

On 2016-02-17 02:32, Justin Lemkul wrote:
>
>
> 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.
>
> -Justin
>
>> 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 -- 
>>> Gromacs
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>

-- 
*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