Re: Hydrogen cut off distance

From: Brian Bennion (
Date: Tue Oct 26 2004 - 12:38:20 CDT

Hello Uday,

There is no hydrogen bond term in the NAMD potential. It only recognizes
these types of interactions as electrostatic pairs. Unless I have missed
an important feature update.

The vmd definition of a hydrogen bond can be changed within vmd for the
dynamic bonds representation. But the definition of distance is from the
oxygen to the donor nitrogen.


 On Mon, 25 Oct 2004, Uday Chippada wrote:

> Hi,
> I have a simple question. When we write the configuration file for the SMD simulation, where do we specify the hydrogen cut off distance.
> I am doing a simulation for 1QSU by fixing one end and pulling on the other end, and I am interested in counting the number of hydrogen bonds that break during the simulation. But I am not sure what hydrogen cut off distance and cut off angle I need to specify while visualizing in VMD.
> Is there an inbuilt cut off distance and angle that NAMD uses while performing the simulation?
> Any help would be appreciated.
> Thank you.
> Sincerely
> Uday Chippada.

**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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