VMD-L Mailing List

From: mohammad rezaei (rezaei.m.p_at_gmail.com)
Date: Wed Jun 24 2020 - 11:35:56 CDT

Dear Giacomo Fiorin

Thanks so much for your suggestion. Yes, I agree with you, I was a little
lazy to find answers about this question. I accepted your advice to read
further and I am so sorry.
I think PMEpot is good because I have point charges.

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

On Wed, Jun 24, 2020 at 6:23 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
>