VMD-L Mailing List

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Mon Jan 27 2020 - 14:20:37 CST

Dear James Kress,
Thanks for the answer. I thought that gmx rdf command just gives the g(r)
as a function of r. I need to plot the number of atoms around a specified
carbon atom.
Kind regards

On Mon, 27 Jan 2020, 20:06 James Kress, <jimkress_58_at_kressworks.org> wrote:

> Why do you not use the gmx rdf function, generate the data file and plot
> it using xmgrace or Excel or any of the other plotting applications
> available? VMD might not be the best choice if all you want to do is a 2D
> plot of the RDF.
>
>
>
> Jim
>
>
>
> James Kress Ph.D., President
>
> The KressWorks® Institute
>
> An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
>
> “*Engineering The Cure*” ©
>
> (248) 573-5499
>
>
>
> Learn More and Donate At:
>
> Website: http://www.kressworks.org
>
> Facebook: https://www.facebook.com/KressWorks.Institute/
>
>
>
> Confidentiality Notice | This e-mail message, including any attachments,
> is for the sole use of the intended recipient(s) and may contain
> confidential or proprietary information. Any unauthorized review, use,
> disclosure or distribution is prohibited. If you are not the intended
> recipient, immediately contact the sender by reply e-mail and destroy all
> copies of the original message.
>
>
>
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> *On Behalf Of *faride
> badalkhani
> *Sent:* Monday, January 27, 2020 7:13 AM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: radial atom distribution
>
>
>
> Dear VMD users
>
> I am simulation a dendrimer using Gromacs software and need to plot the
> number of atoms at a distance (r) from a carbon atom at the center of
> dendrimer core (radial atom distribution). Could you help me how can I
> represent this plot using VMD?
>
> Best regards
>
>
> --
>
> *Farideh Badalkhani-Khamseh*
>
> *Postdoctoral Researcher in Physical Chemistry*
>
> *Tarbiat Modares University*
>