VMD-L Mailing List

From: Gustavo Gust (gust77gust_at_gmail.com)
Date: Tue Oct 27 2009 - 06:48:51 CDT

Dear collegues,

I'm using VMD 1.8.7 and I have a question about the differences between
within and pbwithin.
I need to estimate the number of atoms of oxygen in water around a solute
(radius = 3 Å) and the statement I use in VMD is

set wat [atomselect top "(resname WAT and name O) and pbwithin 3 of (resname
MOL)"]

Using pbwithin I get more oxygen atoms around MOL than using within. The
difference is big in some cases.
I have to take in account the periodical boundary conditions, but using
pbwithin or within is confusing me.

What exactly is the difference between pbwithin and within? In the manual
and comments the explanations is not so clear (I have read the manual).

Thank you in advance,

Gustavo Velardez