[gmx-users] electrical potential using Gromacs

[Andrew DeYoung]

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