Re: Periodic Boundary Condition for a 630 Amino Acid Protein

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Sun Aug 14 2011 - 08:46:11 CDT

Hi Babban,

You box size is going to depend entirely on the spatial extent of your protein (not on the number of amino acids) and the amount of padding you need to ensure that the solute does not interact with its periodic image and that solvent isn't interacting with multiple periodic images of the solute simultaneously, which is going to depend on the cutoffs you use.

As far as the cellBasisVector schemes you show, you should also consider searching the archive of the NAMD mailing list, since this has been asked and answered before.
http://www.ks.uiuc.edu/Research/namd/mailing_list/

You could also just try both schemes and see what happens. The answer should be pretty obvious when you see what happens to the system.

Best wishes,
Josh

On Aug 14, 2011, at 9:15 AM, Babban Mia wrote:

> Hello Everyone
>
> I am doing MD for a 630 Amino Acid Protein and have the following question about PBC:
>
> 1. I am starting off with a folded protein and do not expect it to unfold as such but for a long protein ,a unit cell of 40 A is sufficient ? or Should I consider more ,In most of the cases I have seen 40-50 has been kind of a limit .Please advise
>
> 2. I centered my Protein and my non standard solvent box to origin and thus center of my fully solvate protein system is at around (0,0,0) and the spread of the cell is from X[-20,20],Y[-20 - +20] and Z[-20, 20] as the box I use is 40 A cubical box.
>
> So while giving out values for cell basis Vector , I am getting confused between the following two combinations:
>
>
> cellBasisVector1 40.0 0.0 0.0
> cellBasisVector2 0.0 40.0 0.0 40A ==WHOLE BOX
> cellBasisVector3 0.0 0.0 40.0
> cellOrigin 0.0 0.0 0.0
>
>
> or
>
> cellBasisVector1 20.0 0.0 0.0
> cellBasisVector2 0.0 20.0 0.0
> cellBasisVector3 0.0 0.0 20.0 20A looking at the range/spread of the cell
> cellOrigin 0.0 0.0 0.0
>
>
> Best
> Babban
>

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