VMD-L Mailing List

From: Badmos, Sakiru (sakiru.badmos.14_at_ucl.ac.uk)
Date: Mon Jan 23 2017 - 13:04:44 CST

Hi everyone,

                     I will like to generate the spatial distribution function of water around a solute. I used gmx spatial in Gromacs and I generated the grid.cube following the steps in the manual. When I loaded the grid.cube to VMD, I could view the water around the solute as lines as thus http://imageshack.com/a/img922/9430/1ConqC.jpg but when I changed the drawing method to isosurface, I could only view three hexagonal cubes as thus http://imageshack.com/a/img921/5343/MZgUOq.jpg probably representing the atoms in the central molecule.

 I am confused! I don't understand what is happening. Your help would be highly appreciated.

Thanks