[gmx-users] Re: Can I run BD in water media using Gmx? (Hu Zhongqiao)

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Wed Jan 10 07:22:06 CET 2007

Nobody implied me till now. So that means the current version can not do
BD by implicitly treating water into continuum media, i.e, use of
dielectric constant of water. I hope Gmx developers can help me to make
sure this. Till to now I am been using Gmx and in the near future I need
to do BD for longer time scale. If Gmx can not help, it will be bad.
thanks in advance,
Message: 1
Date: Mon, 8 Jan 2007 18:15:10 +0800
From: "Hu Zhongqiao" <zhongqiao_hu at nus.edu.sg>
Subject: [gmx-users] Can I run BD in water media using Gmx?
To: <gmx-users at gromacs.org>
 <62AAE6335EB82749B7D92E1DFB8B57848BBA44 at MBX21.stu.nus.edu.sg>
Content-Type: text/plain; charset="us-ascii"
Dear users,
I wonder if I can run Brownian Dynamics in water media using Gmx.
Although I know we can set integrator=bd, I dont know how to set
dielectric constant of water in Gmx parameter file. Anyone could give
some hints for this? thanks
Zhongqiao Hu

Zhongqiao Hu
Lab E5-04-27
Tel: 65161946(O)
Department of Chemical and Biomolecular Engineering
National University of Singapore
117576, Singapore
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