[gmx-users] Doubts in visualisation of sdf output

Apramita Chand apramita.chand at gmail.com
Mon Jun 4 19:35:29 CEST 2018

Dear Justin,
Thanks for your reply
You're right. I should be choosing a particular density level for all the
There's another doubt. Why Is it necessary to center the protein before
doing g_spatial?



On 6/4/18 12:04 PM, Apramita Chand wrote:
> Dear Justin,
> Thanks for your reply.
> I followed your suggestion and generated the output for urea SDF
> (gride_urea.cube) and water SDF(grid_water.cube).
> When I visualise both together, I get a picture that is attached in the
> link as follows:
> https://drive.google.com/open?id=1lTF-0pSG4-6p0dQ2W7IQWPiz8CnW5CtO
> The isovalue was found to be 30 for grid_urea.cube while isovalue=20 was
> found to be more suitable for grid_water.cube.
> Is it okay if the isovalues differ?

That depends on what you're doing and what your definition of "suitable"
is. You're choosing two different densities to illustrate different
components. Does that make sense? Are you trying to actually quantify
something or just render an image to show where various things are?


> Thanking you,
> Yours sincerely,
> Apramita

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