From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jul 28 2008 - 06:30:07 CDT

On Mon, 28 Jul 2008, Sue Legge wrote:

hi sue,

SL> A couple of questions regarding solvating a peptide in a cubic box
SL> with periodic boundary conditions,

SL> what exactly is the padding?

a small layer of vacuum around the solute to make sure
that solvent atoms don't get too close to solute atoms.

SL> is it possible to specify an exact box size? Eg. can I create a box
SL> 50x50x50 angstrom?

why do you want that? due to the padding and re-arrangements
during equilibration, your system will have to shrink a bit
to give a meaningful density.

SL> also, is there some way to measure the exact size of the box?

cell size is an input parameter to your simulation. no need to
measure. you just set it.

cheers,
   axel.

SL>
SL> thanks
SL> sue
SL>
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SL> Applied Physics
SL> School of Applied Sciences
SL> Science, Engineering and Technology Portfolio
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
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