VMD-L Mailing List

From: Sebastian Stolzenberg (s.stolzenberg_at_fu-berlin.de)
Date: Mon Sep 22 2014 - 09:59:35 CDT

Dear All,

1.)
In the Solvate Plugin, I came across the
::Solvate::rotate_save_water
procedure, which rotates a given system along the z and x axes to find
the orientation with minimum surrounding cuboid volume V0.
I was wondering why this rotation is not performed along all three
cartesian axes to allow the algorithm to find even smaller values of V0.

As an example, I am attaching a tcl script I wrote to execute this task
for the "2D8R" PDB structure:
As a result, I obtain a 15% reduced volume compared to the one obtained
from ::Solvate::rotate_save_water.
When I further solvate this system with a 20A water buffer layer (not
shown), the total number of atoms is reduced by 29% compared to the
solvated system produced by the solvate plugin.

2.)
At http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/
I read:
"Because the solvation box must be oriented along the cardinal axes,
this can result in significant system size reductions, but should not be
used if the initial orientation was chosen to facilitate analysis"
I don't quite understand the last half sentence, what kind of situations
does it specifically refer to?

Thank you very much, Best,
Sebastian