Re: Prevent DNA denaturation

From: Priyanka Mondal (pmondal_at_udel.edu)
Date: Thu Jun 06 2019 - 08:17:29 CDT

Hi,
you can add harmonic restrain to specific atoms by changing their beta
value. The following tutorial uses that technique on silicon nitride
membrane.
http://bionano.physics.illinois.edu/tutorials/modeling-nanopores-sequencing-dna

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

On Thu, Jun 6, 2019 at 4:45 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp>
wrote:

> 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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