Periodic Boundary Condition for a 630 Amino Acid Protein

From: Babban Mia (babbanmia_at_gmail.com)
Date: Sun Aug 14 2011 - 08:15:28 CDT

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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