Re: how to restrain base pair

From: David A. Case <>
Date: Mon, 28 Apr 2003 12:14:49 -0700

On Mon, Apr 28, 2003, Shuang Ding wrote:

> When I am running MD simulation of 11mer DNA at constant pressure, the two
> strands become apart. So I want to use restraint on Watson-Crick base pairs.
> How to make restraint on base pair?

It should not be necessary to add such restraints for DNA simulations at
room temperature. If your strands are coming apart, there may be some
other problem with the simulation, which should be checked.

If you do need to add restraints, see section 5.9 (pp. 112-116) of the Users'

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Mon Apr 28 2003 - 20:53:01 PDT
Custom Search