From: Takeru KAMEDA (kamedapon_at_hiroshima-u.ac.jp)
Date: Fri Jun 07 2019 - 08:27:26 CDT
Dear all
Thank you for your many advices.
Finally, I employed ssrestraint plugin.
I can perform MD simulation with preventing DNA denaturation.
Best wishes.
Takeru Kameda
PhD Student, Hiroshima University, Japan
________________________________________
$B:9=P?M(B: Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
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$B08_at_h(B: namd-l; Brian Radak
CC: Priyanka Mondal; Takeru KAMEDA
$B7oL>(B: Re: namd-l: Prevent DNA denaturation
The `ssrestraints` plugin in VMD can help you automatically generate extrabonds based restraints for DNA.
On Thu, Jun 6, 2019 at 11:32 AM Brian Radak <brian.radak_at_gmail.com<mailto:brian.radak_at_gmail.com>> wrote:
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<mailto:pmondal_at_udel.edu>> wrote:
Priyanka Mondal,
On Thu, Jun 6, 2019 at 4:45 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>> wrote:
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.
Thank you in advance.
This archive was generated by hypermail 2.1.6
: Tue Dec 31 2019 - 23:20:49 CST
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
Department of Physics and Astronomy,
University of Delaware,
USA
Dear NAMD Users
Thus, I want to restrain the distance between a pair of atoms (C1' atoms in a DNA base-pair).
Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan