Re: hydrogen bonds in NAMD

From: Tim Isgro (
Date: Fri Mar 19 2004 - 11:25:47 CST

Hi Ioana,

The hydrogen bond potential in the Charmm force field is, from what I
gather, viewed skeptically by many people, since there is no very good way
to benchmark the parameters and potential.

"USE HYDROGEN BONDS? NO" states that NAMD is not using the explicit
hydrogen bond potential (default), but the H-bonds themselves will be
covered in the VDW interaction.

To answer Min's original question, a simulation with nucleic acids should
be OK without the explicit H-bond potential.


On Thu, 18 Mar 2004, Ioana Cozmuta wrote:

> Hi,
> I was wondering if anyone replied to the e-mail sent on the namd list
> about the "USE HYDROGEN BONDS NO" message in the namd output file.
> I wonder if it is a force field issue (for example amber embeds the HB
> parameters into the VDW parameters) or if you have to turn something on.
> Thank you,
> Ioana

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