Re: Prevent DNA denaturation

From: Priyanka Mondal (
Date: Thu Jun 06 2019 - 08:17:29 CDT

you can add harmonic restrain to specific atoms by changing their beta
value. The following tutorial uses that technique on silicon nitride

Priyanka Mondal,
Department of Physics and Astronomy,
University of Delaware,

On Thu, Jun 6, 2019 at 4:45 AM Takeru KAMEDA <>

> Dear NAMD Users
> I have a question about how to add the (harmonic) interaction between
> several atoms which I specified.
> I want to restraint each base-pair of double-stranded DNA to prevent
> denaturation.
> Thus, I want to restrain the distance between a pair of atoms (C1' atoms
> in a DNA base-pair).
> Thank you in advance.
> Best wishes,
> Takeru Kameda
> PhD Student, Hiroshima University, Japan

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