From: Axel Kohlmeyer (
Date: Sun Dec 04 2016 - 00:29:54 CST

On Sun, Dec 4, 2016 at 12:38 AM, John Stone <> wrote:
> 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.

it may be worth having a look at packmol.


> Cheers,
> John Stone
> 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
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Phone: 217-244-3349

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.