[gmx-users] electrical potential using Gromacs

[Andrew DeYoung]

Hi Fereshte,

I used PME.

Andrew

-----Original Message-----
From: Fereshte Taherian [mailto:tabasi at csi.tu-darmstadt.de] 
Sent: Saturday, January 04, 2014 5:29 PM
To: Andrew DeYoung
Subject: RE: electrical potential using Gromacs

Hi Andrew,

Many Thanks for your reply. I am checking my system based on your
suggestion.
just one additional question, could you please let me know how did you  
calculate the coulombic interaction in your system, with PME or the  
other methods?

Thanks again,
Fereshte


Quoting "Andrew DeYoung" <adeyoung at andrew.cmu.edu>:

> Hi,
>
> I was able to "fix" the drift in the electric potential by using particle
> decomposition parallelization instead of domain decomposition when running
> the simulations using mdrun (although I still do not know why this "fixes"
> the problem).  Domain decomposition is the default parallelization in
> Gromacs, but particle decomposition can be used with the -pd switch of
> mdrun.  However, I think that particle decomposition is slated to be
removed
> in future versions of Gromacs.
>
> (I also did not use the -correct switch of g_potential, but that alone did
> not fix the problem.)
>
> Happy New Year.
>
> Andrew
>
> -----Original Message-----
> From: Fereshte Taherian [mailto:tabasi at csi.tu-darmstadt.de]
> Sent: Friday, December 27, 2013 8:04 PM
> To: adeyoung at andrew.cmu.edu
> Subject: electrical potential using Gromacs
>
>
>
> Dear Andrew,
>
> I am Fereshte Taherian, and doing my Phd in Technische Universität
> Darmstadt, Germany. Sorry to bother you. Currently I am using Gromacs
> to calculate the electrical potential of a ionic liquid confined
> between two charged surfaces (ewald_geometry = 3dc).
>
> Using g_potential I tried to calculate the potential as following:
>
> g_potential -correct
>
> Looking at the electrical potential, I found a drift in the potential
> as you mentioned in the Gromacs users forum
>
(http://gromacs.5086.x6.nabble.com/Pseudo-2-D-Ewald-Summation-and-Slab-Geome
> try-td4880471.html).
>
> I really appreciate, if you could let me know how did you fix this
problem.
>
> Thank you very much.
>
> I wish you a happy new year.
>
> Best regards,
> Fereshte
>
>
>
>
>
>
> --
> Fereshte Taherin Tabasi
> PhD student of Computational Physical Chemistry
> Center of Smart Interfaces
> Technische Universität Darmstadt
> Petersenstraße 32
> 64287 Darmstadt
> Tel    :(+49)6151-1675040     (Office)
> Fax    :(+49)6151-162048    (university)
>
> Email: tabasi at csi.tu-darmstadt.de
> http://www.csi.tu-darmstadt.de
>
>
>



-- 
Fereshte Taherin Tabasi
PhD student of Computational Physical Chemistry
Center of Smart Interfaces
Technische Universität Darmstadt
Petersenstraße 32
64287 Darmstadt
Tel    :(+49)6151-1675040     (Office)
Fax    :(+49)6151-162048    (university)

Email: tabasi at csi.tu-darmstadt.de
http://www.csi.tu-darmstadt.de