VMD-L Mailing List

From: Ropon-Palacios G. (groponp_at_gmail.com)
Date: Sat Sep 04 2021 - 13:19:49 CDT

Dear users,

 

I have a tetrameric model of an aquaporin with 4 glycerol molecules, which I have already balanced and now I want to generate the windows for the umbrella sampling, I first thought of using SMD to generate the windows, however when I pull not all of them They move in the same position (windows range 1 A), so I thought about moving them manually, but I don't know how to generate all the windows from the balance value, or how could I do it? So I can place the glycerol all in the same position (ie 15 14 13 12 .... 0) inside the aquaporine.

 

 

Thanks for your suggestions.

 

best,

 

Geo.