Subject: SUMMARY: Chemical Programs for Linux

From: Lingran Chen <[email-masked]>
Date: Fri, 7 Feb 1997 09:07:45 -0800

Hi CCL friends:

About two weeks ago I posted here the following question:

> In the past years I used Pentium PC/Linux as a main platform 
> for developing the SYNGEN system
> (http://syngen2.chem.brandeis.edu/syngen.html) and for Web Server.
> I found this PC workstation is just fine. 
>
> And I would like to know how many chemical programs have been ported
> to or developed on Linux and/or how many chemists are using Linux.
> Any information on this question will welcome and I will summarize
> the responses. Thanks.

Thanks a lot for all the responses which are summarized below, as
promised.

However, before offering  the summary, I would like to show you some

======================================================
Interesting Web Sites on LINUX
======================================================

What is Linux? - 
	http://www.ssc.com/linux-int/Introduction/linux.html
What can Linux do? - 
	http://www.ssc.com/linux-int/Introduction/capabilities.html
How many machines have run Linux ? - 

http://www.ssc.com/linux-int/News/Linux/v2.0/PR-Linux.2.0.0-English.html
Where to find other scientific applications on Linux ? -
	http://www.KachinaTech.COM/SAL/
Is Linux as easy to use as Mac OS ? -
	http://www.ssc.com/linux-int/News/linux-pro.html
Is Linux more reliable than commercial UNIX ? -
	http://www.ssc.com/linux-int/Introduction/Usenet/case6.html
Where to obtain Linux ? - 
	http://www.ssc.com/linux-int/Introduction/where.html

======================================================
SUMMARY:  Chemical Programs for Linux
======================================================

From: 
           Wolf-Dietrich Ihlenfeldt <[email-masked]>

Wir haben eine Reihe von Programmen auf Linux laufen,
unter anderem die ganzen CACTVS Tools.

(Please check: http://schiele.organik.uni-erlangen.de/	-Lingran)
---------------------------------------------------------------------------------------------
From: 
        Bryan Van Vliet <[email-masked]>

I have a Linux machine in my home office. I put it together with a
Pentium
motherboard clone and parts from old computers. It is very fast and
nice.
It serves as my firewall/mail server/web server machine. I am using 
Slackware Linux.
---------------------------------------------------------------------------------------------
From: 
        Marcus G Martin <[email-masked]>

We have recently started using a PC with Linux for running our in house 
Gibbs Ensemble - Configurational Bias Monte Carlo code.  We determine 
phase diagrams, among other things, and a single run typically takes a 
week or two of cpu time.  We found it was quite easy to port our code 
(written in fortran) to the Linux system and also get great speed from 
our 200 MHz Pentium Pro.
---------------------------------------------------------------------------------------------
From: 
 	Bill Ross  [email-masked]

People have been running AMBER on linux. See the
benchmarks on our web page for comparison w/
other machines (I'm about to add PPro numbers).

(check: http://www.amber.ucsf.edu/amber/)
---------------------------------------------------------------------------------------------
From: 
        Satyam Priyadarshy <[email-masked]>

Our department have a large number of SGI workstations and 
Dec Alpha workstations. Within last couple of months we have
acquired a couple of Pentium Pro (single and dual processor)
and we are running them with Linux..

The Pro's are faster for quantum calculations cf. R8000 of SGI
using Gaussian.  We are hoping that the use of Linux will grow
in this Department with time and more and more chemistry 
related software will be available.
---------------------------------------------------------------------------------------------
From: 
        Jan Reimers <resrch!janr@wolfe>
   
I am more of a materials scientist with a PhD degree in chemistry.  I
use a Linux/PC system as an inexpensive scientific workstation
for Monte Carlo simulations and electronic structure calculations.
I also find Linux be an excellent environment for software development.
I am currently developing a DFT program for dealing with solids
containing d and f elements.  The program is designed to use a wide
variety of basis functions AO's, Gaussians, contracted gaussians,
plane waves, etc.   I have chosen to use C++ for this
project in order to manage the complexity of the task.  Using an OO
programming approach allows one to abstract away the details of the
various basis functions, so that most of the code has no notion
of precise nature of the basis function it is dealing with.
Linux just happens to come with a C++ compiler (g++-2.7.2), and the
multitasking allows me to do other work while long compilations are
going.
        I currently just pipe (unix pipe concept) data into gnuplot
for plotting.  I have not yet investigated any of the more elaborate 
visualization tools that are available.  I intend to try ViewMol if
a statically linked version becomes available.
        I am very pleased that I can carry out my sort of project at
home without having make a large initial monetary investment in software
(real OS, good compiler, editor, revision control, plotting, etc.)
to get going.  Only 5 years ago this would have been a very expensive
project just to get started on, in terms of OS and development tools.
        It is quite possible that I would benifit from a commercial
C++ compiler, but at the moment g++ is adequite, and it also gaurantees
portability to a very wide variety of platforms.
---------------------------------------------------------------------------------------------
From: 
	Dr. Ir. David van der Spoel     [email-masked]

The GROMACS Molecular Dynamics code runs under linux

http://rugmd0.chem.rug.nl/~gmx

Performance on a 133 MHz pentium is comparable to an SGI Indy
workstation
(MIPS R4600)
---------------------------------------------------------------------------------------------
From: 
            Ezequiel Quintana Morales <[email-masked]>

I use Linux each time that I can. I run Mopac (caculations), Gifa (NMR),
RasMol (viewer), Babel (change bewten file formats).
I think that Linux has a big future ahead.
---------------------------------------------------------------------------------------------
From: 
        "Edward S. Blurock" <[email-masked]>

I am currently porting the REACTION, a system for modeling complex
reaction systems such as combustion mechanisms, to Linux.  It is a C++
application with a JAVA interface.  For more info about REACTION
itself see 

http://info.risc.uni-linz.ac.at:/people/blurock/REACTION/toppage.html
---------------------------------------------------------------------------------------------
From: 
	Carles Bo	[email-masked] (Carles Bo)

 We are porting ADF to Linux.
 check the http://tc.chem.vu.nl/SCM/Welcome.html to get
 more information about ADF.
---------------------------------------------------------------------------------------------
From: 
        "Dr. Teerakiat Kerdcharoen" <[email-masked]>
   
        I also used LINUX/Pentium for production runs of my research
in molecular dynamics simulations. Most of the time, I used in-house
developed codes and sometime public domain source codes from
Daresbury Laboratory library of molecular dynamics softwares in
UK,
        http://www.dl.ac.uk/CCP/CCP5/main.html

        Most of the codes there are written in FORTRAN and certainly
portable to LINUX.
        I would also suggest a Homepage of collection of LINUX's
scientific software at,

        http://www.KachinaTech.COM/SAL/
---------------------------------------------------------------------------------------------
From: 
            "Dr.Larissa Steinhauer" <[email-masked]>

Auf meiner Seite:

http://schiele.organik.uni-erlangen.de/Valentin_Steinhauer

findest Du viele Anwendungen for LINUX und JAVA.
---------------------------------------------------------------------------------------------
From: 
        Margaret Wong <[email-masked]>

We do quite a bit of visualisation, analysis of data and run a web 
server from our linux box.  Nearly anything written in C (with xwindows 
graphics) can be run easily.

---------------------------------------------------------------------------------------------
From: 
        Pedro A M Vazquez <[email-masked]>

We're using FreeBSD (www.freebsd.org) instead of linux but I believe 
most of programs were ported to both as both use the same programing
tools:

        gcc/f2c
        gnu g77
        sun libm
        xfree86
        mesa
        motif
        opengl
        etc

        To my knowledge the following programs are running in both
systems for at least a year

        gamess (even the parallel version)
        gaussian94
        mopac (6,7,93)
        molview
        molden
        rasmol
        mm2 
        mm3

        and many more I can't recall now, these are the most used at my
site. I can't remember a fortran or C program with available source code 
that was unportable to one or another being portable to a mainstream
Unix brand.
        
        As far as I know the only big diference between Linux and
FreeBSD is 
the file size limitation on Linux (2.0G, and presumed to be removed
soon) and 
slightly different behaviours of libm among different distributions
(Slackware,
RedHat, etc) .
---------------------------------------------------------------------------------------------

Thanks.

-Lingran

**********************************************************
Lingran Chen, Ph.D.
Senior Scientific Programmer
MDL Information Systems, Inc.
14600 Catalina Street
San Leandro
CA 94577

Phone: (510) 895-1313, Ext. 1305
FAX:   (510) 614-3616

Email: [email-masked]
URL:   http://www.mdli.com
       http://syngen2.chem.brandeis.edu/~chen/lingran.html
**********************************************************