VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Tue Oct 27 2009 - 09:09:36 CDT

thanks, i didn't even know about this option.

in my understanding the difference in two methods should be essential
for atoms that are close to box boundaries. while within command
operates only within the central cell, the other command takes into
account the next image of the simulation box

On Tue, Oct 27, 2009 at 7:48 AM, Gustavo Gust <gust77gust_at_gmail.com> wrote:
> 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 Ε)  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 

-- 
Roman Petrenko
Physics Department
University of Cincinnati