VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jun 24 2020 - 08:52:23 CDT

Hi Mohammad, compared to your previous message on the LAMMPS mailing list
you have done a marginal amount of additional searching, but you should
read further.

APBS has both its own tutorials (to get started with an example) and
reference manual (to actually understand what the code does). You should
read those, most importantly start by seeing if a Poisson-Boltzmann
computation is what you need for your problem. VMD supports reading and
displaying the output of APBS, but does not produce it on its own.

Alternatively, there is also PMEpot:
http://www.ks.uiuc.edu/Research/vmd/plugins/pmepot/
which will compute the electric field generated from the point charges over
a trajectory. You need to load the atomic point charges in VMD on your own
first.

Giacomo

On Wed, Jun 24, 2020 at 5:03 AM mohammad rezaei <rezaei.m.p_at_gmail.com>
wrote:

> Dear Users VMD
>
> I want to plot a potential map of the electric field of charged gas for a
> specific time of my simulation.
> I use LAMMPS for simulations I read some things about APBS(
> https://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/) or
> Multiwfn +VMD.
> but it is not clear for me.
> Do you have any suggestions?
>
> Best wishes,
> Mohammad
> *Mohammad Rezaei Pandari*
> Ph.D student
> Laser and Plasma Research Institute Shahid Beheshti University
> 1983963113 Evin, Tehran, I.R. Iran
> *t:* + 98 21 2990 4039
> *e:* m_pandari_at_sbu.ac.ir
> *gmail:* rezaei.m.p_at_gmail.com
>
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin