[gmx-users] Doubts in visualisation of sdf output

Justin Lemkul jalemkul at vt.edu
Mon Jun 4 19:23:29 CEST 2018

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
> Message: 6
> Date: Mon, 4 Jun 2018 08:03:21 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Doubts in visualisation of sdf output
> Message-ID: <06a53787-59cc-ff56-ae75-28a49c2d6fa4 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
> On 6/4/18 7:05 AM, Apramita Chand wrote:
>> Dear All,
>> I want the SDF of urea as well as water molecules around my peptide
>> molecule. For this purpose , I used trjconv to get traj1.xtc with -fit
>> rot+trans option(selecting peptide as fitting option and system as
> output).
>> Using this traj1.xtc, I generated traj2.xtc with centering the peptide and
>> again system as output.
>> On this traj2.xtc, I used g_spatial where I selected Peptide molecule for
>> SDF and then water molecules to output coordinates.
> You want the opposite of that - solvent for SDF and peptide for
> coordinate output.
> -Justin
>> The grid.cube files for water and also urea have been formed.
>> However, how do I visualise the peptide molecule along with the
> isosurface?
>> Should I load a separate file containing only centered peptide
> coordinates?
>> Should that be .gro file for the entire trajectory?
>> Please advise.
>> 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


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