Subject: Molecular Dynamics on Biological Molecules.

From: "Iraj Daizadeh" <[email-masked]>
Date: Wed, 15 Oct 1997 08:11:33 -0700

Hello.

Our group has just bought 2 DEC 500 au (low-end workstations) running DEC UNIX
4.0c and we are trying to find computational chemistry software packages that
can calculate classical dynamics of motion for large (circa. 2000+atoms)
biological molecules.  It would be nice if the programs could implement a
Nose/Hoover thermostat and equipped with a variety of force fields such as
amber, ESFF, cff91, etc...  Futhermore, the programs (which may be free or
commercial) must be able to write out trajectories to some sort of archive file
in ascii form for our own calculations.  I will summarize the results as is
customary.

Thanks in advance for all contributions.

Iraj.

-- 
Iraj Daizadeh
Department of Chemistry
University of California
One Shields Ave.
Davis, CA  95616-5295
Phone:  916.754.8695
Fax:    916.752.8995
email:  [email-masked]

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From: "Dr. Bruno Manunza" <[email-masked]>
Date: Wed, 15 Oct 1997 20:00:22 +0100 (NFT)

> Thanks in advance for all contributions.

Dear Iraj, there are several programs doing the things you want. I just 
recall DLPOLY from Daresbury (free after signing a licence), and Amber 
(commercial). You'll find links to the above and several others looking 
throught our software page at http://antas.agraria.uniss.it
go there an then click the Computational Chemistry Software link.
You'll find some info also in the molmod page

Hope it helps
regards
Bruno

Dr Bruno Manunza
DISAABA (Dept. of Agricultural Environm. Sci)
University of Sassari
V.le Italia 39
07100 Sassari, ITALY
phone: 39 79 229215
fax:   39 79 229276
e-mail: [email-masked]
e-mail: [email-masked]
e-mail: [email-masked]
web: http://antas.agraria.uniss.it

---

From: Rick Venable <[email-masked]>
Date: Wed, 15 Oct 1997 17:54:09 -0400 (EDT)

> in ascii form for our own calculations.  I will summarize the results as is

I know that the DEC Alpha is one of the platforms supported by the
academic version of CHARMM; it does have Nose/Hoover, can easily handle
30,000 atoms or more, and individual coordinate frames from a trajectory
can be easily written in the CHARMM ASCII format, or in PDB format.  It's
not so great at supporting other force fields, for a variety of reasons
(some technical).  The academic version is available for a modest fee via
the Karplus group at Harvard;  for more info see

	http://yuri.harvard.edu

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
[email-masked]  |    \  /  |=|    position of the FDA; for that,
http://nmr1.cber.nih.gov/           \/   |=|    see   http://www.fda.gov  )