Re: Re: Maximum and minimum box size

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Mon Feb 15 2021 - 18:09:20 CST

Hi Raman,

NAMD can support all-atom simulations of up to 2 billion atoms.

If I’m doing my units conversion correctly (always my downfall), a 50 nm cubed box would be expected to contain about 12.5 M atoms or about 4.167 M water molecules. This is fine for NAMD but depends also on the hardware you have available. CG using MARTINI would reduce this 1/4 (4 AA waters for 1 CG water, right?).

As to the minimum box size, each dimension of the periodic cell must be at least pairlistdist (defaults to cutoff) plus hgroupCutoff (defaults to 2.5 A) plus margin (defaults to 0).

Best regards,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801
dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/
> On Feb 12, 2021, at 4:35 AM, Raman Preet Singh <ramanpreetsingh_at_hotmail.com> wrote:
> 
> Dear NAMD Community,
> 
> Reposting the question in case someone might help me.
> 
> Regards,
> RPS
> 
> Get Outlook for Android <https://urldefense.com/v3/__https://aka.ms/ghei36__;!!DZ3fjg!vrgVBqtMmgoUULzcCyouJL5QtkVTHxBaefJa8qknVVFu0-biOEFeTY09kDyH2P1-fg$>
> From: Raman Preet Singh
> Sent: Monday, January 18, 2021 11:46:42 PM
> To: NAMD list <namd-l_at_ks.uiuc.edu>
> Subject: Maximum and minimum box size
>  
> Dear All,
> 
> I am interested in performing a simulation where one of the box dimensions is expected to reach 50 nm. I have seen publications with 20+ nm water box sides but not sure if 50 nm or higher dimensions are supported in NAMD. I will be using MARTINI CG models. If 50 nm is supported, do I need to make any changes in the NAMD conf file?
> 
> A related question is: what is the minimum box size supported? A 1 nm distance from the sides of the solute is the ideal situation. However, if it is just a solvent box, what is the minimum supported size (for AA and CG models)?
> 
> Thank you in advance for your time and inputs.
> 
> Regards,
> Raman
> 
> 

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