From laaksone@csc.fi  Sat Jan 25 04:18:43 1997
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From: Leif Laaksonen <laaksone@csc.fi>
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To: Konrad Hinsen <hinsen@ibs.ibs.fr>
cc: berriz@chasma.harvard.edu, chemistry@www.ccl.net
Subject: Re: CCL:Quanta, Alphas & Xterms (Was: "Running Quanta remotely" & "Quanta on AlphaStation clones?")
In-Reply-To: <199701241813.TAA18572@lmspc2.ibs.fr>
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Hi,

I myself believe that X and X terminals are almost obsolete in the sence
of molecular modelling. Today we have OpenGL (as pointed out by Konrad
Hinsen) which is available for almost any thinkable hardware. The problem
still is the graphical user interface. By using for example Tcl/Tk and
OpenGL it is possible to write modelling applications that run on all
platforms from Windows NT/95 to Unix boxes. 

The whole modelling business is in deep problem because it would be
possible to run all the commercial modelling applications on inexpensive
PC:s but it would be impossible for the commercial software houses to
charge the horrifying prices we have to pay today for the software because
the PC:s are so inexpensive and noone would pay five times more for the
software than for the hardware. In fact I see the reluctance, by the
software houses, to port applications to the DEC platform as the last
desperate attempt to only support Unix versions, because DEC is also
active in the Win NT field.

To clearify my opinion I'm not working for DEC and I don't even
collaborate with them but I believe they have a sound attitude.

Regards,

-leif laaksonen

On Fri, 24 Jan 1997, Konrad Hinsen wrote:

> > it).  I tend to associate this narrow hardware dependance with the
> > personal computer world; it seems to me extraordinary (not to say
> > archaic) by Unix world standards.  I guess I'm an idealist...
> 
> Writing portable graphics applications used to be a nightmare, and
> even today it remains difficult. Before OpenGL (which isn't that old)
> there was no 3d graphics library which could pretend to be powerful
> enough and universal. And even OpenGL is not generally usable via X
> terminals.  I guess we'll have to wait a few more years before remote
> (and efficient!) use of 3d graphics programs becomes standard.
> 
> Right now the most reasonable option would be to provide each program
> in two versions: one using optimized OpenGL for local graphics hardware,
> and one using Mesa for remote use. That's for example the approach used
> by VRweb (a free VRML viewer).
> 
> I find the lack of Alpha support more surprising, given the popularity
> of Alphas today. But it is not untypical for commercial Unix software
> to be available on selected systems only. Keeping several ports up to
> date and providing support for it is, after all, an expensive task.
> Having a clear market dominance makes the decision to limit systems
> even easier. In fact, this is one of the main arguments for free
> software in the sense of the FSF: anyone is free to port such programs
> to any hardware, so it has a good chance of happening.
> 
> -- 
> -------------------------------------------------------------------------------
> Konrad Hinsen                          | E-Mail: hinsen@ibs.ibs.fr
> Laboratoire de Dynamique Moleculaire   | Tel.: +33-4.76.88.99.28
> Institut de Biologie Structurale       | Fax:  +33-4.76.88.54.94
> 41, av. des Martyrs                    | Deutsch/Esperanto/English/
> 38027 Grenoble Cedex 1, France         | Nederlands/Francais
> -------------------------------------------------------------------------------
> 
> -------This is added Automatically by the Software--------
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>              Web: http://www.ccl.net/chemistry.html 
> 
> 

-------------------------------------------------------------------
Leif Laaksonen                     |  
Center for Scientific Computing    | Phone:      358 9 4572378
P.O. Box 405                       | Mobile:     358 400425203
FIN-02101 Espoo                    | Telefax:    358 9 4572302
FINLAND                            | Mail:  Leif.Laaksonen@csc.fi
-------- URL: http://laaksonen.csc.fi/leif.laaksonen.html ---------




From luca@lcfs.chim.unifi.it  Sat Jan 25 06:18:43 1997
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 25 Jan 1997 11:55:29 +0100 (MET)
Date: Sat, 25 Jan 1997 12:00:21 +0100
From: Luca Pedocchi <luca@lcfs.chim.unifi.it>
Subject: again IPs
Sender: root@CESIT1.UNIFI.IT
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Sirs, maybe my quetion was not clearly posed. I didn't ask theoretical
information on HOW to calculate IPs, I already did it by myself and
published a couple of papers with delta-SCF, generalized ground state
and so on. I already knew papers from Chong and I already dealt with IPs
of adsorbed CO on metal clusters. I did it with deMon, a pretty good DFT
code from Montreal, and I had interest in the challenge deMon -
Gaussian. The final answer seems to me the following: with gaussian94 it
is impossible to localize a hole in a molecular orbital. Is it correct?
And please, no more teaching.
Regards
                  Luca
-- 
Dr. Luca Pedocchi
Laboratorio di Chimica Fisica delle Interfasi
via Cavour, 82 - 50129 Firenze - ITALY

http://lcfs.chim.unifi.it/solid/pedocchi
e-mail luca@lcfs.chim.unifi.it

phone +39-55-2757793
fax   +39-55-219802

Non esistono uomini cattivi, se sono cucinati bene
                                            (Stefano Benni)

From jkl@ccl.net  Sat Jan 25 12:29:48 1997
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To: chemistry@www.ccl.net
Subject: Please, more teaching...
In-Reply-To: Mail from 'Luca Pedocchi <luca@lcfs.chim.unifi.it>'
      dated: Sat, 25 Jan 1997 12:00:21 +0100
Cc: jkl@ccl.net



Dear Brothers and Sisters in CCL...

Your coordinator speaking... (as usually off topic...). Commenting on the
last line of one of the messages (WHICH IS, I ADMIT TAKEN OUT OF
THE CONTEXT -- Sorry about it!!!):

      > And please, no more teaching.

Ou contraire!!!  Please, do a lot of teaching!!! We have a lot of
people on the list who are interested in background too...
If you have some overviews, hand-outs, cheat-sheets, software, any
usefull stuff in the context of CCL,  please post it to the list
(if it is short), or deposit materials in archives of CCL (contact me any
time if you have questions...). Please share and have a nice feeling
of doing good in the time when science and education is often about money
(nothing wrong with it, but let us also have some fun in the process,
and keep our souls well nourished... We are the intelectual cream,
we do it for the humanity, aren't we?. You bet we are, even if there is
a price tag...).

This is not to start a flame war, but just a friendly reminder that
many of us enjoy the education which is brought by the list. Myself included.
So, do not be hesitant to include the background info in your message.
We have students and educators, and newbies, and we teach and have our niches
and want to learn more... No, this is not about pushing the list to
a highschool level, but about sharing... Not everybody is an expert in
everything, and it is nice to have general idea, and know whom to ask...
And for those of us who are pragmatic (we all are...): It is nothing wrong
with generating the need, and then feeling it up, and generating a new one.
We are a step ahead, aren't we? 
And if you want to learn? -- Please ask good questions... I am sure I motivated
some people. I am a nice fellow and a jovial person, and do motivation well.
And if you have collected your answers, please make a summary (trim the
headers, long signatures, and try to cut the redundant info), and post it
to the list. I enjoy them -- I hope more people do too...

Thanks and sorry... Please, do not continue this topic on the list.
It is my job to so soul searching here, so do not get into unfair
competition {:-)}.

Jan Labanowski
jkl@ccl.net

P.S. Yes, we work on improving infrastructure and the contents of the
list quite intensively, and we will have some goodies at spring time...


From yu@infiniti.wavefun.com  Sat Jan 25 15:18:46 1997
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From: "Jianguo Yu" <yu@infiniti.wavefun.com>
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Date: Sat, 25 Jan 1997 12:03:17 -0800
Reply-To: yu@wavefun.com
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To: CHEMISTRY@www.ccl.net
Subject: Re: How to implement new parameters in MOPAC 6.0
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On Jan 24,  6:33am, Gabriele Costantino wrote:
> Subject: CCL:M:How to implement new parameters in MOPAC 6.0
> Hi CCL friends:
> just a simple question. I would like to add a new element to Mopac 6.0 (i.e
Fe
> or Rh). I have modified the block.f routine by adding the new PM3 parameter
> definition (USS, USP....). When tested on a simple compound, however, the
> program stops with the message "DATA ARE NOT AVAILABLE FOR ELEMENT ...".
> The same thing happens if the EXTERNAL keyword is added to force the program
to
> read an external parameter files.
> Any suggestion will be welcome
> Thanks
>
> Renato Rovito
> Undegraduate student
> Universita' di Perugia (Italy)
>
> -------This is added Automatically by the Software--------
> -- Original Sender Envelope Address: gabri@iris.chimfarm.unipg.it
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>              Web: http://www.ccl.net/chemistry.html
>
>-- End of excerpt from Gabriele Costantino

In my knowledge, it's difficult (even impossible) to add parameters for Fe and
Rh into MOPAC, because in MOPAC, atoms can't hold d orbitals, but for the
transition metals, as Fe and Rh, the d functions are essential. I think the
logic structure of MOPAC can't go to transition metals even you only plan to
calculate s and p orbitals for them (like you did).

There exists a few of semiempirical programs being able to calculate transition
metal compounds with d orbitals, such as MNDO93, AMPAC, ZINDO and our SPARTAN.
If you want to calculate the transition metal compounds, yuo may need to choose
from above programs.

Jianguo Yu

-- 
+-----------------------+------------------+-------------------------+
|Jianguo Yu, Ph.D.      |  ______________  | E-Mail: yu@wavefun.com  |
|Computational Chemist  |  \  _________ /  | Phone:  (714)955-2120   |
|Wavefunction Inc.      |   \ \\\\\\\\/    | Fax:    (714)955-2118   |
|18401 Von Karman       |    \ \\\\\/      | "The doctrines observe  |
|Suite 370              |     \ \\/        |  nature"                |
|Irvine, CA 92612       |      \/          |   Lao-tzu (604-531 B.C.)| 
+-----------------------+------------------+-------------------------+




From D.van.der.Spoel@chem.rug.nl  Sat Jan 25 17:18:49 1997
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Subject: Quanta etc.
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Hi Modellers.

The last few days, a lot of messages about the use of Quanta on
non-SGI machines appeared on the CCL.  We have quanta running
on a dedicated SGI box, and I tried to run it over the net once,
setting the display to another SGI machine. This does work, but
it is useless, because it is horrendously slow.
The main conclusion from the postings in my opinion therefore is:
Quanta is usable only on your local SGI box

Although we have a lot of SGIs around our lab, and they work nicely,
they are certainly not the fastest workstations you can buy. Furthermore,
there are many alternatives to large parts of Quanta in public domain 
(FREE) software packages.

Although these packages may require some more work to get running,
but you can run the software on any machine you like.  Some examples:
Visualisation: check out VMD (http://www.ks.uiuc.edu)
Molecular Dynamics: check out GROMACS (http://rugmd0.chem.rug.nl/~gmx)
Ab Initio: check out GAMESS 
To conclude, spend your money on fast hardware, so you can do more science.

David,
________________________________________________________________________
Dr. Ir. David van der Spoel	Dept. of Biophysical Chemistry
s-mail:	Nijenborgh 4, 9747 AG Groningen, The Netherlands.
e-mail:	spoel@chem.rug.nl	www:	http://rugmd0.chem.rug.nl/~spoel
phone:	31-50-3634327		fax: 	31-50-3634800
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

From d3g359@fido.pnl.gov  Sat Jan 25 19:18:49 1997
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Date: Sat, 25 Jan 1997 15:27:19 -0800
From: d3g359@fido.pnl.gov (John Nicholas)
Subject: TiO2
To: CHEMISTRY@www.ccl.net
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All, I have been looking for ab initio and DFT calculations
on TiO2 (the molecule). So far journal and databases searches
find nothing. Anybody doing work on this molecule or know
of published calculations?

Thanks, John

------------------------------------------------------------------------------
  John Nicholas                                 Office: (509) 375-6559
  Senior Research Scientist                        FAX: (509) 375-6631
  Environmental Molecular Sciences Laboratory     
  Pacific Northwest National Laboratory
  Mailstop K1-96
  Richland, WA 99352
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From d3g359@fido.pnl.gov  Sat Jan 25 19:26:33 1997
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From: d3g359@fido.pnl.gov (John Nicholas)
Subject: BhandhLYP
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All, what is the current opinion on the Becke half and half LYP functional?

It appears that this functional is not in keeping with the
theory reported in Becke's original "half-and half" (JCP) paper.

I notice that Gaussian eliminated this option from the current verion.

Any comments?



------------------------------------------------------------------------------
  John Nicholas                                 Office: (509) 375-6559
  Senior Research Scientist                        FAX: (509) 375-6631
  Environmental Molecular Sciences Laboratory     
  Pacific Northwest National Laboratory
  Mailstop K1-96
  Richland, WA 99352
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From ccl@www.ccl.net  Fri Jan 24 11:18:34 1997
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Date: Fri, 24 Jan 1997 12:28:38 -0330 (NST)
From: Uli Salzner <uli@smaug.physics.mun.ca>
To: ccl <chemistry@ccl.net>
Subject: g94/DFT
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Hi everybody,

using the DFT user defined methods in G94, user's reference p.61-62, 
I am trying to construct something like a half/half functional. From 
the B3LYP description (p.61) I gather the coefficients to be:

0.8 for Slater, 0.2 for HF, 0.72 for Becke, 0.19 for VWN, and 0.81 
for LYP.

If I transfer this to the formula below I get:
P1=1.0, P2=0.2, P3=0.72, P4=0.8, P5=0.81, and P6=0.19

According to the B3LYP example on p. 62 the coefficients should be:
P1=1.0, P2=0.8, P3=0.2, P4=0.72, P5=0.19, and P6=0.81

My question is, have I mixed up something or is there a problem with 
this example? Since it would lead to fatal errors, if I got these 
coefficients mixed up, I would be very grateful for commends.

Thanks in advance,
Uli

Ulrike Salzner
Department of Chemistry
Memorial University of Newfoundland
St. Johns, NF A1B 2N5
Canada

Tel.: (709) 737-2151
Email:uli@smaug.physics.mun.ca




From L330%SUEARN2.BITNET@mps.ohio-state.edu  Fri Jan 24 15:18:34 1997
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 24 Jan 1997 14:22:48 -0500 (EST)
Date: Fri, 24 Jan 1997 22:18 +0000 (MSK)
Subject: G-94 time for DEC Alpha / HP server
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       Sorry, do somebody know the G-94  test 178  run times for
 DEC Alpha 8200/8400 ( any frequency ) and  HP server S - class ,
 especially for more than  one processor .

                     Nick



From walt@panix.com  Fri Jan 24 15:46:50 1997
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Date: Fri, 24 Jan 1997 14:52:55 -0500 (EST)
From: Walter Polkosnik <walt@panix.com>
To: Gabriel Berriz <berriz@chasma.harvard.edu>
cc: chemistry@www.ccl.net
Subject: Re: CCL:Quanta, Alphas & Xterms (Was: "Running Quanta remotely" & "Quanta on AlphaStation clones?")
In-Reply-To: <9701241439.AA24925@chasma.harvard.edu>
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On Fri, 24 Jan 1997, Gabriel Berriz wrote:

> 
> This sure is a confusing issue.  I recall hearing before something
> like what you write here, and I have had some e-mail responses along
> the same lines as yours, but below are a couple excerpts from e-mail
> sent to me by two different MSI folks in response to this CCL query:
> 
>    As far as running Quanta remotely, this can *not* be done using
>    X emulation.  We had, at some time in the past, done some work
>    running Quanta with DGL, and the core visualization seemed to
>    run fine, but it was quite slow, and there were difficulties with
>    a lot of the more expert functions.
> 
>    ...QUANTA will not work over X, it requires local graphics
>    hardware.
> 

I was responding with my experience with earlier verions of Quanta, I
wasn't aware they removed this facility in the latest version. I don't
remeber any difficulties with the 'expert' functions (whatever they are),
but I do remeber it being slow at times, mainly when accessing it from
another building - but this was probably due to the network. Whenever I was
on the local ethernet segment things didn't seem much slower at all.

It's too bad it's not supported at all anymore, it's very useful to be able
to do things remotely at times.

In fact, I know a lab which has gone over to exactly your scheme (servers +
X terminals), but fortunately they use other software. 

--
Walter Polkosnik                             walt@panix.com  
Physics Department                           http://www.physics.qc.edu/~walt
Queens College, City University of New York  (718)-997-3364 voice
Credo quia absurdum est.                     (718)-997-3349 fax



From ccl@www.ccl.net  Fri Jan 24 22:18:38 1997
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Date: Fri, 24 Jan 1997 21:34:26 -0500 (EST)
From: Walter Polkosnik <walt@panix.com>
To: chemistry@ccl.net
Subject: Quanta and X terminals
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On Fri, 24 Jan 1997, Dr. David N. Haney wrote:


> > Of course, this is the whole point of X-windows. I have run Quanta in
> > essentially this manner. You may want to worry about speed of the net
> > connections between the server and X-terminals (graphics updating can be
> > slow depending on the network).
> 
> I don't think this works unless you are running on a DGL machine thru X.
> If you try this from a PC (no DGL) then you get lots of DGL errors.  Perhaps
> this is not the case with the Alpha version of Quanta.
> 

Yes, I forgot to add that whatever X terminals you use have to support DGL.
I haven't found a PC X server that supports it yet either.

--
Walter Polkosnik                             walt@panix.com  
Physics Department                           http://www.physics.qc.edu/~walt
Queens College, City University of New York  (718)-997-3364 voice
Credo quia absurdum est.                     (718)-997-3349 fax



From soriano+@pitt.edu  Sat Jan 25 16:18:49 1997
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From: David  Soriano <soriano+@pitt.edu>
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To: Jan Labanowski <jkl@ccl.net>
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Subject: Re: CCL:Please, more teaching...
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Hi Jan:


I would ask all forum members that are involved in aspects of molecular
modeling, emphasis on bio-active molecules, to please e-mail me
information on software they are currently using. I will be compiling this
information for inclusion in a, page linked to Dr. Heelis' new journal:
"Internet Journal of Science : Bilogical Chemistry". Thank you , Dave
Soriano Ph.D. Pitt's Bradford campus in Pa. U.S.A.


 




























