From: Justin Gullingsrud (
Date: Sun Jul 27 2003 - 23:58:21 CDT


On Sun, Jul 27, 2003 at 09:34:03PM +0200, Vlad Cojocaru wrote:

> Dear VMD and NAMD users,
> I am trying to get some answers about namd. I dont know if there is a
> maillist for NAMD. I have questions regarding:

You can mail the NAMD developers at, though there is not
a "namd-l" list like there is for VMD.

> 1. The TIP3P water model from Amber (the angle H-O-H is not maintained
> during the simulation) and I was wondering if applying constraints on
> this angle would solve the problem.

Yes, specifying "rigidBonds water" will constraint the water geometry,
including the angle. Specifying "rigidBonds all" constrains all bonds
to hydrogens.

> 2. The manual is very scarce regarding the temperature coupling scheme
> and I was wondering how to apply the same protocol as in Amber when
> using "ntt=1" and "tautp=2.0"?

I'm not sure what those parameters do in Amber, but I'm forwarding your
question on to the other NAMD developers in case they know.


> I was trying to send this questions to the maillist but couldnt find.
> I would appreciate any answer,
> Thanks
> Vlad
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1327
> e-mail:
> home tel: ++49-551-9963204

  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys