Re: Periodic Boundary Condition for a 630 Amino Acid Protein

From: Babban Mia (babbanmia_at_gmail.com)
Date: Sun Aug 14 2011 - 09:19:18 CDT

Thanks Joshua :)
I am using a Non standard Solvent Box and when I tried to play around with
different values of padding for Non Standard Box, The solvation set up did
not change at all which I guess is obvious because It is not going to add
water molecules by itself if you are using your own non standard solvent
box.

Is this true ?
or Padding can be changed even if one is using a non standard solvent box.

For eg: MyNonstandard box is 40A and I was using a very small peptide for
sample and on changing the padding from 5-20 ,The solvation setup looked the
same;
Any comments?

Thanks for the PBC info

Best
Babban

On Sun, Aug 14, 2011 at 7:16 PM, Joshua Adelman <jla65_at_pitt.edu> wrote:

> 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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