From raman $#at#$ bioc01.uthscsa.edu  Thu Jun 10 15:54:26 1993
From: raman \\at// bioc01.uthscsa.edu (C.S.RAMAN)
Message-Id: <9306110154.AA09743 ^at^ bioc01.uthscsa.edu>
Subject: MOLECULAR DYNAMICS - mailing lists, etc.
To: chemistry "at@at" ccl.net
Date: Thu, 10 Jun 1993 20:54:26 -0500 (CDT)


Dear Netters

As promised here is the blurb about MD mailing list in addition to
information on new MD programs!

1. Some of you must already be familiar with Andreas Windemuth's program MD
for doing molecular dynamics simulations on macromolecules.  It is
extremely well written code (in C) and provides the newcomer with
insight into what MD is all about.  For those of you who are unaware of
this program, you can FTP the same from:

lisboa.ks.uiuc.edu

The programs are in compressed form (*.Z) in the directory /pub/md/

Users implementing the results obtained from this program in their
manuscripts are requested to cite the following references:

a) Board, J.A., et al. [1992] Chem.Phys.Lett. 198, 89
b) Windemuth, A. and Schulten, K. [1991] Molecular Simulation 5,353

2.  Klaus Schulten's group is also developing a program which will
include (in the near future!) capabilities to view the trajectories
created by MD.  This program is called VRCHEM and is available for FTP
from the same site mentioned above!  

look in the directory /pub/vrchem

3.  MD Mailing List!  :)

There is good bit of interest in a program like MD and as the field
develops, there is a need for dissemination of ideas and inprovements!
During a recent conversation with Andreas, I indicated to him
that there is substantial interest in the Biomolecular Structure
community for his program.  This, in addition to the Parallelized
version of MD (PMD, which Andreas is developing now!) prompted him to
setup a mailing list (on June 8, 1993) whose purpose is the following:

        Distribute the PMD program to be tested by various users and
   receive feedback; at the same time, let users share their experiences
   and discuss improvements to the code.  NOTE: Andreas does not provide
   support for PMD at this time.  

" PMD is a scalable, parallel program for the simulation of the dynamics
of biological macromolecules.  Its force field is related to programs
such as CHARMM, EXPLOR, GROMOS, DISCOVER and others. Emphasis is placed
on improved algorithms to significantly enhance efficiency of the
simulation of biological macromolecules, without sacrificing long range
interactions"

I would strongly urge those interested in Molecular Dynamics to
subscribe to this mailing-list and contibute to the same.  Although, in
its present implementation, the list is for questions and discussions
related to  PMD, I don't see why one could not discuss general md
related issues there.  In any case, here is how you subscribe to the
list: 

send mail to:

pmd-request { *at * } cumbnd.bioc.columbia.edu

Request that your name be added to the mailing list!  That should do...


You can also download PMD by FTP'ing to:

cumbnd.bioc.columbia.edu

the files are located in /pmd/

I hope that this posting (at least transiently!) quenches the thirst for
increased discussion in the MD community!

Cheers
-raman
-- 
C.S.Raman                                 raman()at()bioc01.uthscsa.edu - Internet
UNIX Programming & Administration         70412.2354 "-at-" compuserve.com - CIS
SPARC & SGI Systems                       raman -8 at 8- hermes.chpc.utexas.edu - CHPC
Department of Biochemistry                craman(-(at)-)launchpad.unc.edu
UTHSCSA       
7703 Floyd Curl Dr.                       (210) 567-6623   [Tel]
San Antonio, TX 78284-7760                (210) 567-6595   [Fax]
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         If a man's wit be wandering, let him study the Mathematics
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