VMD-L Mailing List
From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Sun Jul 27 2003 - 23:58:21 CDT
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Hi,
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 namd_at_ks.uiuc.edu, 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.
Cheers,
Justin
> 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: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> 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
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