VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Dec 03 2016 - 23:38:11 CST

Hi,
  If you haven't received any other suggestions yet, I thought I'd
comment very briefly.

A conceptually straightforward approach to do this might be to
compute an expanded molecular surface mesh (padding out the probe radius
significantly) on which to place particles, followed by the use a simple
monte carlo approach to pushing the particles around to achieve perfectly
uniform spacing. Perhaps someone has an existing tool/code to suggest, but
I don't know of one personally.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Dec 03, 2016 at 03:55:50AM +0000, Ebert Maximilian wrote:
> Hi there,
>
> I am looking for a method to place evenly n-molecules at m-angstroem from the protein surface. is there any easy solution to this? before I start coding I was wondering if this is already solved.
>
> Thanks a lot!
> Max 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/