Re: LJ Parameters for Au and S and harmonic constraints

From: Jeff Comer (
Date: Fri Apr 08 2016 - 12:52:50 CDT

You might find this paper helpful:


Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Fri, Apr 8, 2016 at 2:18 AM, Madhulika Gupta
<> wrote:
> Hello everyone,
> I need to simulate sulphur and gold in NAMD. Can someone help me with the LJ
> parameters for Au and S. I have looked up the literature and and no two
> papers use the same LJ values.
> Also if I need to hold Au fixed, I know that one method is fixedAtoms in
> NAMD and the other is using harmonic constraints.Please also let me know as
> to what to write in the .conf file to hold Au atoms fixed using harmonic
> constraints.
> Any help will be very useful to clear my confusion.
> Thanks
> Madhulika Gupta
> --
> Madhulika Gupta
> Research Scholar
> Department of Chemistry
> Indian Institute of Technology, Delhi
> New Delhi-110016

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