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