Subject: Summary: Molecular Dynamics on Biological Molecules.

From: "Iraj Daizadeh" <[email-masked]>
Date: Tue, 21 Oct 1997 12:35:54 -0700

Hello.

Well, it has been more than one week since the first email went out concerning
software that is able to simulate classical dynamics for biomolecules on a DEC
500 au workstation.  The outline of this summary is as follows: First the
original question is stated.  Then in chronological order all replies are
presented [email addresses and other information concerning the whereabouts of
the original authors (besides their names) have been deleted].

Thanks to everyone that applied and all those that are interested.

Iraj.

-------------------------------------------------------

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.
--------------------------------------------------------
1.

NAMD currently doesn't have support for DEC UNIX, and it only uses
Charmm force field. NAMD runs on
a variety of other platforms, though, and it should not be difficult
to make a port to DEC, provided you have pvm on your machines.
Otherwise, NAMD can simulate systems of large size (the largest test we did
was about 500,000 atoms, and there are production simulations for systems
of 32,000 atoms), maintain the temperature of the system in the simulation,
and write trajectory files.

VMD, on the other hand is a stand alone visualization and analysis program
which can be used with a variety of file formats and can work with
simulation trajectories.

Sincerely,

Sergei Izrailev

2)

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 Manunza

3)

Checkout the GROMACS code
http://rugmd0.chem.rug.nl/~gmx

It is definitely the fastest code on workstations for MD.

Groeten, David.

4)

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

5)

Have you tried the Amber suite of programs, or any of the Biosym software?
Details for both should be easily found on the web.

Clare Bostock-Smith

6)

Dear Iraj,
	Here at Reading we use DLPOLY which is a free licensed
MD software developed by Smith and Forester at Daresbury Labs in
Northern England.  It can do all you ask for and more :)  It is
written in Fortran and can be compiled for any number of architectures
and requirements. I have found is immensely better than any
commercially available software.  I am not sure about its use outside
the UK - it is written by people working for one of the research
councils here in the UK and it is free for people working in the UK
who sign a contract saying what they are working on - i.e. for non
commercial gain etc.

check out
http://gserv1.dl.ac.uk/TCSC/Software/DL_POLY/main.html
for more details and get back to me if I cna be of more help.
Tim
--
Tim Astley

7)

Dear Iraj,
One of the OMG software products you might be interested is AMBER. Please
check the following sites for more information:

http://www.oxmol.com
http://www.amber.ucsf.edu/amber/amber.html

Thank you for your inquiry and please let us know if we can be of help in
anyway.
Sincerely,
NT Ton

8)

		   1. Since we have access to source code and since the program
is
   written from what I can see in Python, how difficult would it be to
   write the dynamics trajectory snap shot by snap-shot to a file in either
   .pdb or .bgf form?  Has this been done by someone else?

Converting a trajectory files to a series of PDB files is very
easy. I don't know .bgf, so I can't comment on it. Generating
a trajectory directly as PDB files is more difficult, but doable.

		   2. What force fields does MMTK come?  Would it be difficult
to add new
   forcefields.

Amber94 is implemented; others can easily be added, but there is
no documentation (yet) on how to do it.

		   3. Can this program work on a DEC 500 au running DECK UNIX
4.0C?

I see no reason why it shouldn't work, but I didn't test it on such
a machine. Basically all Unix flavours should work.

You should have come t the Python conference in San JOse (wjere
I am right now; I have given a talk plus demonstrtions of
MMTK...

Konrad Hinsen
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------

-- 
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]