Re: Prevent DNA denaturation

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Jun 06 2019 - 10:27:29 CDT

For atom groups, you can use colvars. For specific atom interactions I
would recommend extraBonds. You can read about both in the user guide.

HTH,
BKR

On Thu, Jun 6, 2019 at 9:19 AM Priyanka Mondal <pmondal_at_udel.edu> wrote:

> 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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