VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Dec 04 2016 - 00:29:54 CST
On Sun, Dec 4, 2016 at 12:38 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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.
> 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!
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.