[gmx-users] Doubts in visualisation of sdf output

Apramita Chand apramita.chand at gmail.com
Mon Jun 4 18:04:21 CEST 2018

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:

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?

Thanking you,
Yours sincerely,

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
> 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.


> The grid.cube files for water and also urea have been formed.
> However, how do I visualise the peptide molecule along with the
> Should I load a separate file containing only centered peptide
> 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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