[gmx-users] Doubts in visualisation of sdf output

Justin Lemkul jalemkul at vt.edu
Mon Jun 4 20:23:38 CEST 2018

On 6/4/18 1:35 PM, Apramita Chand wrote:
> Dear Justin,
> Thanks for your reply
> You're right. I should be choosing a particular density level for all the
> components.
> There's another doubt. Why Is it necessary to center the protein before
> doing g_spatial?

You need a frame of reference for the output to make any sense. You want 
to know the density of given atoms around some solute, so if the solute 
is freely rotating and translating, the output doesn't make sense. If 
it's fit to remove overall global motion, the calculation means something.


> Thanks
> Apramita
> 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?
> -Justin
>> Thanking you,
>> Yours sincerely,
>> Apramita


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list