VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sun Dec 04 2016 - 11:17:09 CST

Another option would be insert-molecules from the GROMACS toolset. It
can add a number of molecules at positions you specify, or just place N
molecules randomly such that they are minimum radius away from your
solute. See http://manual.gromacs.org/programs/gmx-insert-molecules.html

-Josh

On 12/04/2016 12:24 AM, Axel Kohlmeyer wrote:
> On Sun, Dec 4, 2016 at 12:38 AM, John Stone <johns_at_ks.uiuc.edu> 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.
>
> axel.
>
>> 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
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>>
>
>