[gmx-users] electrical potential using Gromacs
adeyoung at andrew.cmu.edu
Sat Jan 4 19:01:40 CET 2014
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.
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
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:
Looking at the electrical potential, I found a drift in the potential
as you mentioned in the Gromacs users forum
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.
Fereshte Taherin Tabasi
PhD student of Computational Physical Chemistry
Center of Smart Interfaces
Technische Universität Darmstadt
Tel :(+49)6151-1675040 (Office)
Fax :(+49)6151-162048 (university)
Email: tabasi at csi.tu-darmstadt.de
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