From chemistry-request@www.ccl.net  Mon Aug 17 08:03:25 1998
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Date: Mon, 17 Aug 1998 08:53:54 -0300 (EST)
From: Sergio Augusto Jardino Filho <sjardino@iq.usp.br>
To: chemistry@www.ccl.net
Subject: Stability calculation
Message-ID: <Pine.SOL.3.91.980817084951.1997A@quim>
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Dear CCL,

I have a basic question: How can I compare the stability of two molecules 
with different number of atoms using the energy result of a CBS 
calculation or another kind of single point calculation?

Thanks is advance

Sergio A. Jardino Filho
Univesidade de Sao Paulo
Brazil


From chemistry-request@www.ccl.net  Thu Aug 13 04:01:12 1998
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From: Xiangyun Guo <xiangyun@tu-harburg.de>
To: chemistry@www.ccl.net
Subject: Diffusion within irregular pores



Dear all

I am investigating the diffusion in pores with fractal walls
by the Monte Carlo method. Could anyone give me some references
on the effect of fractal pores on diffusivity ?
Thank you in advance.

Xiangyun GUO
Email: xiangyun@tu-harburg.de 
----------------------------------
E-Mail: Xiangyun Guo <xiangyun@tu-harburg.de>
Date: 13-Aug-98
Time: 09:53:46

This message was sent by XFMail
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From chemistry-request@www.ccl.net  Thu Aug 13 05:14:05 1998
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From: shin@hermes.fju.edu.tw (Shin-Inn Chen)
Message-Id: <9808130837.AA15982@hermes.fju.edu.tw>
To: chemistry@www.ccl.net
Subject: water dimer anion



dear friends:
      i would to ask about references of water dimer anion (H2O)2- in both
 theoretical and experimemtal sides. 
      any suggestion will be greatly appreciated!
 
e-mail: shin@hermes.fju.edu.tw                            shin 1998/8/13


From chemistry-request@www.ccl.net  Thu Aug 13 13:39:19 1998
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 13 Aug 1998 14:41:40 GMT-3
Date: Thu, 13 Aug 1998 14:32:09 -0300
From: Gerd Bruno Rocha <gbr@NPD.UFPE.BR>
Subject: Rational function molecular integrals
To: CHEMISTRY@www.ccl.net
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Dear Netters,

I am looking for molecular integrals of rational exponential type
orbitals of the form:

	f(r) = P(r)*exp(-alpha*r)/(1 + alpha*r)

where P(r) is a Laguerre polynomial of r.

If any of you know of any reference about that, at least for the formula
of overlap integrals for these functions, please let me know. 
I'll summarize replies.

Thank you all

Gerd Bruno Rocha

DSc Student in Computational Chemistry 

E-Mail : gbr@npd.ufpe.br          
       : gerd@simas.dqf.ufpe.br
                  
Universidade Federal de Pernambuco
Centro de Ciencias Exatas e da Natureza
Departamento de Quimica Fundamental
Recife - PE - Brazil                                    
http://www.dqf.ufpe.br


From chemistry-request@www.ccl.net  Thu Aug 13 14:50:09 1998
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From: "David Baker" <dbaker@siue.edu>
To: <chemistry@www.ccl.net>
Subject: Higher Order Saddle Points
Date: Thu, 13 Aug 1998 13:55:02 -0500
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I am currently studying the transition state structures that arise during
the inversion of 6-membered ring systems. These systems exhibit various
degrees of the anomeric effect. Although the majority of the higher energy
saddle points (half-chairs) are first order, a few contain a second (25-75
cm^-1) imaginary vibrational frequency. I realize that flexible rotors,
methyl groups, and floppy rings sometimes demonstrate this behavior.

(Hehre, W.H. Practical Strategies for Electronic Structure Calculations;
Wavefunction: Irvine, 1995, 96)

However, I've noticed that the rms gradient for structures having 2
imaginary frequencies is slightly higher than for those containing 1. Many
times it is necessary to loosen the convergence criteria in order to get an
optimization to a saddle point to finish. The GAMESS User's Guide states
that an OPTTOL value of 0.0005 is the largest that a person would want to
use.

(GAMESS User's Guide, 4 May 98 edition, p 4-38)

This means that the maximum component of the gradient has to be less than
0.0005 and the rms gradient has to be less than (1/3)OPTTOL or 0.000167. My
higher order saddle points would require an OPTTOL value in the range
(0.0006, 0.0007). This would correspond to a rms gradient of (0.0002,
0.00023).

While I've read many good journal articles that report finding transition
states for other ring systems, they rarely list the convergence criterion
used in the calculation. The reason for this is obvious. The purpose of
performing these calculations is not to produce and report gradients but to
obtain and report useful properties of structures.

My questions are listed below:

1.) In general, are rms gradients for higher order saddle points of ring
structures larger than those with only 1 imaginary frequency?

2.) What is considered to be a maximum acceptable rms gradient for
transition states of larger systems? (>20 atoms)

My next question has to do with higher order saddle points, such as monkey
saddle points and so on.

3.) I've read papers by Hehre, Pople, Pulay, Murrell, and Laidler that
discuss the properties of saddle points. However, I would like to know what
others think about higher order saddle points. In other words, do higher
order saddle points actually exist for real potential energy surfaces, or
are they artifacts introduced by the limitations of various level of theory?

I'll produce a summary of responses after an accepted time period.

Sincerely,

David Baker dbaker@siue.edu




From chemistry-request@www.ccl.net  Thu Aug 13 17:08:41 1998
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Date: Thu, 13 Aug 1998 17:10:04 -0400
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Dear CCL Members,

AHSystems Group's web site is now at www.ahsystem.com.  Please bookmark
it.

Thank you.

John Parikh
AHSystems Group
5401 Lakeford Ln.
Suite L-1
Bowie, MD 20720
301.352.0896   Ph
301.352.0199   Fx
www.ahsystem.com




From chemistry-request@www.ccl.net  Thu Aug 13 19:36:19 1998
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Date: Fri, 14 Aug 1998 09:35:27 +1000
From: Drake Diedrich <Drake.Diedrich@anu.edu.au>
To:  "CHEMISTRY@www.ccl.net" <CHEMISTRY@www.ccl.net>
Subject: Re: CCL:rasmol problem
Mail-Followup-To: Fenglou Mao <mao@csb0.IPC.PKU.EDU.CN>,
	"CHEMISTRY@www.ccl.net" <CHEMISTRY@www.ccl.net>
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In-Reply-To: <Pine.SGI.3.91.980813092932.3259A-100000@csb0.IPC.PKU.EDU.CN>; from Fenglou Mao on Thu, Aug 13, 1998 at 09:32:16AM -0700




On Thu, Aug 13, 1998 at 09:32:16AM -0700, Fenglou Mao wrote:
> 
> Dear all,
>      When I run rasmol in my linux box, it always tells me:
>                "No suitable DISPLAY!"
>      Had someone meet this problem? And how to solve it?

   Rasmol defaults to an 8 bit display.  The XFree86 server that ships with
Linux can only handle one bit depth at a time.  You probably have true color
(24 or 32 bit) or hi-color (15 or 16 bits).  There are flags, probably in
the Makefile to compile Rasmol for other bit depths.

-- 
Dr. Drake Diedrich, Research Officer - Computing, (02)6279-8302
John Curtin School of Medical Research, Australian National University 0200
Replies to other than Drake.Diedrich@anu.edu.au will be routed off-planet


From chemistry-request@www.ccl.net  Thu Aug 13 22:01:24 1998
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Date: Thu, 13 Aug 1998 22:01:25 -0400 (EDT)
From: Shiang-Tai Lin <stlin@UDel.Edu>
Reply-To: Shiang-Tai Lin <stlin@UDel.Edu>
To: Computational Chemistry List <chemistry@www.ccl.net>
Subject: Solvation calculation in Gaussian 94
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Dear CCL users,

I was trying to use G94 to do some solvation calculations and
had difficulty in understanding the meanings of some of the 
output lines. I appreciate any of your help.

In the input file, I wrote
#T rhf/6-31g(d) scrf=ipcm volume test

The output due to the keyword "volume" are

 Box volume = 2398.137 fraction occupied=1.000
 Molar volume = 2398.137 bohr**3/mol (214.007 cm**3/mol)
 Recommended a0 for SCRF calculation =  5.34 angstrom ( 10.08 bohr)

Question (1): What's the shape of the box?
Question (2): How to calculate a0 from the molar volume?
              It seems to me that the formula
              (molar volume/Pi)^(1/3)+0.94 bohr
              is used. But why?

The some of the output due to scrf=ipcm are

 Max. Dist. Between Center of Nuclear Charge and Isosurface = 5.222190E+00
 Min. Dist. Between Center of Nuclear Charge and Isosurface = 3.402845E+00
 Total "Solvent Accessible Surface Area" of Solute = 2.467157E+02
 Volume of Solute Cavity = 3.391144E+02

Question (3): What are the units of these values?
Question (4): Where can I find references that explains how to calculate
              these values?

Thank you.

Shiang-Tai
Department of Chemical Engineering
University of Delaware
(O) (302) 831-6857
(H) (302) 368-8388
E-mail: stlin@udel.edu





From chemistry-request@www.ccl.net  Fri Aug 14 06:23:58 1998
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From: Viorel Chihaia <vchihaia@chimfiz.icf.ro>
To: chemistry@www.ccl.net
Subject: Point Charges in GAMESS (fwd)
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---------- Forwarded message ----------
Date: Fri, 14 Aug 1998 12:00:05 +0300 (EEST)
From: Viorel Chihaia <vchihaia@chimfiz.icf.ro>
To: MARYJO@nev.edu
Subject: Point Charges in GAMESS

Hello MARYJO,

I have consulted only now the "ccl" letters and I have seen your
letter. I made point charges in GAMESS. It is easy: you
create a fictive atom (or more) without basis and with ECP
with zero any ECP parametres ( coefficients and potentials)
and with a charge for core which you want.

Try this solution and if you have problems I will send you a concret
example.

With best regards,

Viorel Chihaia
Institute of Physical Chemistry
Surface Science and Catalysis Lab.
Bucharest, Romania
e-mail: vchihaia@chimfiz.icf.ro




From chemistry-request@www.ccl.net  Fri Aug 14 10:24:59 1998
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Hi

We are buying some new PCs for a computer lav for the students. We are
thinking about buying some voodoo2 graphic cards to try to run some
real graphics program using mesa and xfree86.

Has anyone any experience with this ?
What programs have people tried (O, whatif, xtalview)

thanks for any information

yours

arne

--Multipart_Fri_Aug_14_16:25:45_1998-1
Content-Type: text/plain; charset=US-ASCII

---------------------------------------------------------------------------
              The more I use Windows, the more I love Linux
---------------------------------------------------------------------------
 Arne Elofsson     arne@biokemi.su.se http://www.biokemi.su.se/~arne/
 Tel:+46(0)8-161553      Dept of Biochemistry, Stockholm University
 Fax:+46(0)8-153679	 10691 Stockholm, Sweden

--Multipart_Fri_Aug_14_16:25:45_1998-1--


From chemistry-request@www.ccl.net  Fri Aug 14 13:04:35 1998
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From: shin@hermes.fju.edu.tw (Shin-Inn Chen)
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To: chemistry@www.ccl.net
Subject: basis set
Status: RO
Content-Length: 547



dear netters:
     i have two questions about basis sets:

    1) does any one know Sadlej`s medium-sized polarized basis sets reported 
in Theor. Chim. Acta 1991, 79, p123 ? and would you please send me a copy in 
Gaussian format for element O and H? since i have some problems for finding
the reference. 
    2) which basis set is excellent for reproducing dipole moment and
polarizability of molecules, especially water?
      
      thanks a lot for your help!

e-mail: shin@hermes.fju.edu.tw                            shin   1998/8/15     


From chemistry-request@www.ccl.net  Fri Aug 14 12:07:06 1998
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Date: Fri, 14 Aug 1998 12:06:50 -0400 (EDT)
From: Sergei Tretiak <serg@markov.chem.rochester.edu>
To: "'CCL'" <CHEMISTRY@www.ccl.net>
Subject: Re: CCL:Xwindows terminal emulator
In-Reply-To: <01BDC611.75C880A0@zinc.unomaha.edu>
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Dear Douglas,

You may try PC-Xware from NCD for Win3.1,95(98),NT 
(https://www.ncd.com/ppcx/ppcx.html). NCD suggested price is $395, but 
probably you can get it cheaper from other soft. retailers. 

Probably, this is the best product on the 
market. At least it works perfectly well on ours PC. Xwindows terminal 
emulator is very good, e.g. running remote Spartan 5.0 from SGI IRIX is 
very fast. 

		Sincerely,
				Sergei

 .-----------------------------------------------------------------------.
|\  / \	|		Sergei Tretiak                          | / \  /| 
|.\/...\|.......................................................|/...\/.|
| Department of Chemistry     | Voice: (716) 275-8289                   |
| University of Rochester     | Fax:   (716) 473-6889                   | 
| P. O. Box 270216            | E-mail: serg@markov.chem.rochester.edu  |
| Rochester, NY 14627-0216    |         serg@wigner.chem.rochester.edu  |
|    Homepage: http://markov.chem.rochester.edu/serg/welcome.html       |
|_______________________________________________________________________|

On Wed, 12 Aug 1998, Douglas E. Stack wrote:

> 
> Our department will be adding some new Win98 PC.  I'd like to install a Xwindows terminal emulator on each.  My only experience with such products has been with Exdous by White Pine.  Does anyone have a preference for a good, inexpensive Xwindows emulator for running modeling programs from SGI workstations?
> 
> Thanks in advance for any suggestions.
> 
> Douglas E. Stack	
> Assistant Professor
> Department of Chemistry
> University of Nebraska at Omaha
> Omaha, NE 68182-0109
> (402) 554-3647
> (402) 544-3888 (fax)
> destack@unomaha.edu
> 
> 
> 
> ---
> Administrivia: This message is automatically appended by the mail exploder:
> CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator
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> 



From chemistry-request@www.ccl.net  Fri Aug 14 12:22:11 1998
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Dear Colleagues,
                            I am interested in using Wien97
to do some MD - DFT simulations with Uranium
and Plutonium compounds.  Unfortunately, I cannot get
through to the web site for information or
contact names.  Can any one tell me which elements are
supported (specifically if U and Pu are
supported) and if it is feasible to do MD DFT with this
FP-LAPW code on clusters or cells with
around 4 U atoms/ions and 8 oxide ions?
        Thanks in advance for any help.
                    Cheers,
                                    Dave

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

Dr. David W. Price,       Tel: +44 (0)118 9875123  extn 7415
Department of Chemistry,  Fax: +44 (0)118 9316331
University of Reading,    mailto:d.w.price@reading.ac.uk
Whiteknights,
READING                http://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html
RG6 6AD
U.K.

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





From chemistry-request@www.ccl.net  Fri Aug 14 12:58:43 1998
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Date: Fri, 14 Aug 1998 09:58:17 -0700 (PDT)
From: "Ricky A. Kendall" <ra_kendall@pnl.gov>
Subject: Re: CCL:Xwindows terminal emulator
In-reply-to: <01BDC611.75C880A0@zinc.unomaha.edu> (destack@unomaha.edu)
To: CHEMISTRY@www.ccl.net
Reply-to: ra_kendall@pnl.gov
Message-id: <199808141658.JAA09368@cagle.emsl.pnl.gov>




  > Date: Wed, 12 Aug 1998 16:51:31 -0500
  > From: "Douglas E. Stack" <destack@unomaha.edu>
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  > 
  > Our department will be adding some new Win98 PC.  I'd like to install
  > a Xwindows terminal emulator on each.  My only experience with such
  > products has been with Exdous by White Pine.  Does anyone have a
  > preference for a good, inexpensive Xwindows emulator for running
  > modeling programs from SGI workstations?
  > 
  > 
  > Thanks in advance for any suggestions.
  > 
  > Douglas E. Stack	
  > Assistant Professor
  > Department of Chemistry
  > University of Nebraska at Omaha
  > Omaha, NE 68182-0109
  > (402) 554-3647
  > (402) 544-3888 (fax)
  > destack@unomaha.edu
  > 
  > 
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  > 

I have used two different x-windows programs under Win3.1/95/98; they
are X-Remote from NCD and EXCEED from Hummingbird.  Both are in the
$500 range so I don't know if you would call that expensive or not.
The latter also sells a companion product that allows OpenGL to work
as well.  The street price if you look around for the EXCEED products
you can get them for $300/$150 roughly.  I got both EXCEED products
(X/GL) for less $500 a few months back.  The Hummingbird product works
well on the net and over a modem.  The X-Remote software needs a
"server" function either on a terminal server or on a remote
workstation.  It is harder to configure etc but it is solid as
well (once you get it working).  I would recommend the EXCEED product
if you can afford the cost.  You could also dual-boot Linux and then
have a decent X system; if you need OpenGL support then you would have to
buy that I think?  There might be a free OpenGL system but I don't
know of one.  Things change so fast with Linux it is difficult to keep
up. 

Hope this helps :)


Regards,
Ricky

-- 

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===    Ricky A. Kendall  <internet: ra_kendall@pnl.gov>                   ===
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