From krys.radacki@ac.rwth-aachen.de  Tue May 12 10:30:40 1998
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Date: Tue, 12 May 1998 13:30:45 +0000
From: Krzysztof Radacki <krys.radacki@ac.rwth-aachen.de>
Subject: G94: MaxCycle ?
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Dear CCL'ers
I've set in my input line SCF=(MaxCycle=100)
How should I understand  such a line in Gaussian log file:

"Number of steps in this run= 37 maximum allowed number of steps= 100.

It means that Gaussian will calculated up to 37 steps or 100?

--
Krzys Radacki

krys.radacki@ac.rwth-aachen.de




From desingh@mailbox.syr.edu Tue May 12 13:03 EDT 1998
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From: Deepak  Singh <desingh@mailbox.syr.edu>
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Hi everyone,

	Could people who have had experience with both tell me which is
better where interaction with CHARMM (running in batch mose) is concerned.
In my experience, INSIGHT97 is more powerful, but especially where CHARMM
is concerned, QUANTA is more convenient.  

Regards


Deepak.


--------------------------------------------------------------------------------
Deepak Singh
Grad Asst, Dept. of Chemistry,                                  
1-014 Scitech, Syracuse University, 
Syracuse,NY 13244.                                         
Tel: 315-443 1739
Fax: 315-443 4070
e-mail: desingh@mailbox.syr.edu   	URL : http://web.syr.edu/~desingh


.............and the Sun was eclipsed by the Moon.
--------------------------------------------------------------------------------




From yubofan@guomai.sh.cn  Mon May 11 04:30:16 1998
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Date: Mon, 11 May 1998 15:56:06 +0800
From: Yubo Fan <yubofan@guomai.sh.cn>
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Organization: Department of Chemistry, Fudan University
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Hi,

I am doing an geometry optimization of phenylferrocene but failed. I
used G94W to get optimized ferrocene geometry by B3LYP/LanL2DZ first,
than added a Phenyl to substitute a hydrogen atom of ferrocene by a
molecular visualization software and got a PDB file. Finally, I changed
this PDB file into Gaussian Z-Matrix file. I list this file below. But
G94W cannot get a converged result.

Could anyone give me some help and advice? Why didn't G94W converge?

%chk=PhFecene.chk
#P B3LYP/LanL2MB OPT SCF=(QC, Direct, Save) Test

Phenylferrocene

   0   1
 C
 C,1,R2
 C,1,R3,2,A3
 H,1,R4,2,A4,3,D4,0
 Fe,1,R5,2,A5,3,D5,0
 C,2,R6,1,A6,3,D6,0
 C,3,R7,1,A7,2,D7,0
 H,2,R8,1,A8,6,D8,0
 H,3,R9,1,A9,7,D9,0
 C,5,R10,1,A10,2,D10,0
 C,5,R11,1,A11,10,D11,0
 C,5,R12,1,A12,10,D12,0
 C,5,R13,1,A13,10,D13,0
 C,5,R14,1,A14,10,D14,0
 C,7,R15,3,A15,1,D15,0
 H,6,R16,2,A16,1,D16,0
 H,10,R17,5,A17,1,D17,0
 H,11,R18,5,A18,1,D18,0
 H,12,R19,5,A19,1,D19,0
 H,13,R20,5,A20,1,D20,0
 H,14,R21,5,A21,1,D21,0
 C,15,R22,7,A22,3,D22,0
 C,15,R23,7,A23,22,D23,0
 C,22,R24,15,A24,7,D24,0
 C,23,R25,15,A25,7,D25,0
 H,22,R26,15,A26,24,D26,0
 H,23,R27,15,A27,25,D27,0
 C,24,R28,22,A28,15,D28,0
 H,24,R29,22,A29,28,D29,0
 H,25,R30,23,A30,15,D30,0
 H,28,R31,24,A31,22,D31,0
      Variables:
 R2=1.41028905
 R3=1.41150901
 R4=1.07844269
 R5=2.14614904
 R6=1.41120836
 R7=1.42246435
 R8=1.07825195
 R9=1.07624259
 R10=2.14903773
 R11=2.14683386
 R12=2.14795357
 R13=2.1501648
 R14=2.14973218
 R15=1.50455508
 R16=1.07624191
 R17=1.07869814
 R18=1.07850946
 R19=1.07849943
 R20=1.07862056
 R21=1.0784372
 R22=1.40057318
 R23=1.39977369
 R24=1.38688224
 R25=1.38741306
 R26=1.08470353
 R27=1.08487411
 R28=1.38709537
 R29=1.08690938
 R30=1.08687696
 R31=1.08655024
 A3=107.95009396
 A4=125.88932932
 A5=70.80337296
 A6=107.93731491
 A7=108.79998552
 A8=125.94504633
 A9=125.16181076
 A10=179.84385592
 A11=141.67180659
 A12=115.67707903
 A13=115.61551298
 A14=141.45550996
 A15=126.70838917
 A16=125.172042
 A17=127.90053239
 A18=128.30037256
 A19=128.37599769
 A20=128.43243698
 A21=127.97068892
 A22=121.1641715
 A23=121.13599997
 A24=121.1330814
 A25=121.11803197
 A26=119.84422277
 A27=119.83149768
 A28=120.36001927
 A29=119.62918272
 A30=119.60496644
 A31=120.30885096
 D4=-175.5911137
 D5=61.26033664
 D6=-0.08264602
 D7=-0.18885303
 D8=175.63229645
 D9=-175.19814914
 D10=60.33677873
 D11=119.60128994
 D12=82.10047866
 D13=39.32853924
 D14=1.85528911
 D15=-175.90933534
 D16=175.06444747
 D17=-119.33543583
 D18=59.07149566
 D19=21.67646152
 D20=-21.27859676
 D21=-58.98598014
 D22=176.85946022
 D23=-178.72031418
 D24=-179.40338784
 D25=179.24484277
 D26=-179.55725767
 D27=179.74588886
 D28=0.49741098
 D29=179.62313218
 D30=179.8483037
 D31=-179.99770853

--Link1--
%chk=PhFecene.chk
#P B3LYP/LanL2DZ GEOM=CheckPoint OPT=ReadFC SCF=(Direct, Save) Test

Phenylferrocene

   0   1

With best wishes

Y. Fan

--
=============================================================
Yubo Fan                         Email: yubofan@guomai.sh.cn
Organic Synthesis Lab                   yubofan@fudan.edu.cn
The Department of Chemistry
Fudan University                 Phone: 8621-65648139
No. 220 Handan Road              Fax:   8621-65641740
Shanghai, 200433
P. R. China
=============================================================




From fgonzale@lauca.usach.cl  Mon May 11 12:30:20 1998
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Date: Mon, 11 May 1998 11:34:29 -0400
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Hi all!

    Anybody know how can I do a "restart" to a G2PM2 calculation?,
the calculation was stopped by full disk, around 2 Gb occupated...... If
it is not possible to make a restart for this job, how can I do  a
similar calculation for obtaining Proton Affinities PA using G94W?.

Thanks a lot!

Danilo///

--
Fernando Danilo González Nilo
University of Santiago de Chile, Faculty of Chemistry and Biology,
Computational Chemistry Lab.
Casilla 40, Correo 33, Santiago-CHILE
Phone: (562) 681 2575-Anexo:799 ; Fax: (562) 681 2108
URL   : http://quimbio.usach.cl/~danilo/
E-mail: fgonzale@lauca.usach.cl
===================================================================


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From jomal@chaer.iq.ufrj.br  Tue May 12 16:30:35 1998
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To: chemistry@www.ccl.net
Subject: CCL: Re:Cannot optimize phenylferrocene



	Dear Yubo,

	In my opinion, if you wish to optimize all geometric 
parameters it is better to use cartesian coordinates rather than
Z-matrix. The z-matrix must be misdefined.

							-Joao

From rochaj@rpi.edu  Tue May 12 18:30:34 1998
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From: "John-David R. Rocha" <rochaj@rpi.edu>
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Dear CCLers,

I am looking to perform some ab initio calculations on small (2-6 atoms)
Fe, Pb, and As containing neutral molecules.  I have experience with HF
calculations using Gaussian9x.  Are there 6-31g* and higher quality
basis sets available for these heavy metals?  If so where can I find
them.  I've seen a number of papers concerning heavy metal DFT
calculations.  Where could I find basis sets that include Fe, Pb, and As
that would be optimized for DFT.

In both cases (HF and DFT), I'm interested in calculating energies and
frequencies for mapping PESs of simple bimolecular reactions to study
their kinetics.  I would appreciate any help the CCL could supply.

Regards
John-David

-- 
John-David Ray Rocha
Rensselaer Polytechnic Institute
rochaj@rpi.edu
http://www.rpi.edu/~rochaj

From sergei@ks.uiuc.edu  Tue May 12 19:30:37 1998
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From: "Sergei Izrailev" <sergei@ks.uiuc.edu>
Message-Id: <980512183233.ZM16396@glasgow.ks.uiuc.edu>
Date: Tue, 12 May 1998 18:32:32 -0500
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To: chemistry@www.ccl.net
Subject: VMD 1.2b2 is now available
Cc: vmd@ks.uiuc.edu
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Content-Type: text/plain; charset=us-ascii


        Announcing version 1.2b2 release of VMD
        ---------------------------------------

The Theoretical Biophysics group at the University of Illinois and the
Beckman Institute would like to announce the availability of version
1.2b2 of the program VMD, a package for the vizualization and analysis
of biomolecular systems.  This software is being made available to the
structural biology research community free of charge, and includes the
source code for VMD, documentation, and precompiled binaries for SGIs,
HPs, Solaris 2, and Linux.  The documentation (still being updated)
includes an installation guide, a users guide, and a programmers guide
for interested researchers.  VMD also provides on-line help through
the use of an external HTML viewer.

A full description of VMD is available via the VMD WWW home page:
        http://www.ks.uiuc.edu/Research/vmd/

New in this version
-------------------

 o VMD has been ported to Sun Solaris 2.
 o Upgraded to Linux RedHat 5.0
 o OpenGL support works with native HP-UX and Sun OpenGL
   implementations
 o Added Tk support and upraded to Tcl/Tk 8.0
 o Upgraded to Babel 1.6
 o Added support for MSMS, a program for calculating molecular surfaces
 o Added support for Grasp file format
 o For most commands, typing in a command without arguments will
   print a help message
 o Added more commands to Tcl scripting interface
 o Many bug fixes

Version 1.2b1 features
----------------------

 o This biggest improvement in version 1.2b1 support for
     platforms other than GL-based SGIs.  In addition to the full
     source and SGI binary distributions, VMD is now available
     for HP-UX (tested under 9 and 10) and Linux.

 o Greatly enhanced Tcl scripting commands for performing
     molecular analysis, writing scripts, developing tutorials,
     etc.

 o New rendering styles, a fast (and cheap) solvent
     accessible surface and C-alpha and P trace method, and
     improvements to the existing styles.

 o New output renderer formats: Postscript, VRML and STL (a
     stereo-lithography format)

 o Support for Amber structure and animation file formats


 =============   Basic information about VMD   =================

Features
--------

  VMD  is designed  for  the visualization and  analysis of biological
  systems such as proteins,  nucleic acids, lipid  bilayer assemblies,
  etc.  It may be used to view more general molecules, as VMD can read
  standard Protein  Data Bank  (PDB)  files and  display the contained
  structure.  VMD provides a wide variety of methods for rendering and
  coloring a  molecule:  simple  points  and  lines,  CPK  spheres and
  cylinders, licorice bonds,    backbone tubes  and  ribbons,  cartoon
  drawings,  and others.  VMD can be  used  to animate and analyze the
  trajectory of a molecular dynamics  (MD) simulation.  In particular,
  VMD can act as a  graphical front end  for an external MD program by
  displaying  and animating a    molecule undergoing simulation on   a
  remote computer.

The program has many features, which include:
    o No limits on the number of molecules, atoms, residues or
      number of animation frames, excepting available memory.
    o Many molecular rendering and coloring methods.
    o Stereo display capability.
    o Extensive atom selection syntax for choosing subsets of atoms for
      display (includes boolean operators, regular expressions, and
      more).
    o Integration with the program 'Babel' which allows VMD to read many
      molecular data file formats.  Even without the use of Babel,
      VMD can read PDB files, as well as CHARMM- and X-PLOR compatible
      binary DCD files and X-PLOR compatible PSF files.
    o Ability to write the current image to a file  which may be
      processed by a number of popular raytracing and image rendering
      packages, including POV-Ray, Rayshade, Raster3D, and Radiance.
    o Extensive graphical and text-based user interfaces, which use the
      Tcl package to provide full scripting capabilities.
    o Extensions to the Tcl language which enable researchers to write
      their own routines for molecular analysis
    o Modular, extensible source code using an object-oriented design in
      C++, with a programmer's guide describing the source code
    o Integration with the program NAMD, a fast, parallel, and scalable
      molecular dynamics program developed in conjunction with VMD
      in the Theoretical Biophysics Group at the University of Illinois.
      See the NAMD WWW home page for more info:
             http://www.ks.uiuc.edu/Research/namd/

      VMD can be used to set up and concurrently display a MD simulation
      using NAMD.  The two programs, along with the intermediary
      communcations package (called MDComm) constitute the 'MDScope'
      environment.

Availability
------------

The software is available for downloading from
http://www.ks.uiuc.edu/Research/vmd/

Please email any questions to vmd@ks.uiuc.edu.

  VMD, NAMD, and the entire MDScope environment are part of
an ongoing project within the Theoretical Biophysics group
to help provide free, effective tools for molecular dynamics
studies in structural biology.  For more information, see
http://www.ks.uiuc.edu/Research/MDScope/.  This project is
funded by the National Institutes of Health (grant number
PHS 5 P41 RR05969) and the Roy J. Carver Charitable Trust.

                                                Sergei Izrailev
                                                vmd@ks.uiuc.edu
                                                May 12, 1998

-- 


From smori@utsc3.chem.s.u-tokyo.ac.jp  Tue May 12 23:30:37 1998
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To: chemistry@www.ccl.net
From: smori@utsc3.chem.s.u-tokyo.ac.jp (Seiji Mori)
Subject: B3LYP and HF MO differences-Summary
Cc: bear@ellington.Pharmacy.arizona.edu


Thank you for the two responses,
from Prof. C. J. Cramer and Dr.G. Schreckenbach.
I guess that a few paper reported on the comparison between HF and B3LYP MO
energies,
I do not know the published reports for organometallics.

We also found the phenomena of HF FMO energies lower than B3LYP FMO energies
for Me2Cu- and MeCu species (S. Mori and E. Nakamura, submitted for Theochem
(Special Issue for Prof. Morokuma's 65th birth)).

Seiji Mori

Original question
At 2:54 PM 98.4.27, Seiji Mori wrote:
> Dear netters:
>
>
> I had not posted to CCL for a long time.
>
> By the way, I am now quitely interested in the energy level differences
> between HF and DFT.
>
> In the Oct,1997, Dr. Schreckenbach summarized questions about the DFT MO
> energies
>  and learned much about this.
> I learned from a review (Bareands and Gritsenko, JPC, 1997, 101, 5383 )  and a
> paper (Salzner, et al. J. Comp. Chem. 1997, 18, 1943)
> but the former review is not written about hybrid functionals and the
> latter written about the olefin.
> Dr. Politzer  said in the summaries
> that they submitted the Theoretical Chemical Account  , but I do not know
> whether this is already published.
> I would like to know the difference between HF orbitals and Kohn-Sham MOs
> with the hybrid
> method as to organometallic compounds.
>
> Is it generally known that HF HOMO energy (HOMO-1.. also) is lower than
> B3LYP HOMO
> (or HOMO-1..)energy?
>
> Do you know the additional references about these topics?
>
> Kohn-Sham "one-electron" orbitals of B3PW91, B3LYP.. methods should include
> the component of
> electron-correlation.
> There may exist a problem of comparisons of the energy level of
>  Kohn-Sham MO among the systems of different number of
> electrons (for example, ethylene and butadiene, MeAu and MeCu)
>
> I would like to know about this. I will summarize the answers.
>
> Sincerely yours,
> Seiji Mori
>
>
---Answer from Georg Schreckenbach---
Mime-Version: 1.0
Date: Mon, 27 Apr 1998 10:09:28 -0600
To: smori@utsc3.chem.s.u-tokyo.ac.jp (Seiji Mori)
From: schrecke@t12.lanl.gov (Georg Schreckenbach)
Subject: Re: CCL:B3LYP and HF MO differences

Dear Seiji:

you have cited my recent CCL query (I have placed the summary also at my
website:
http://www.t12.lanl.gov/~schrecke/research.DIR/CCL_DFTMOEnergies.html), and
I am interested in your summary, as you can imagine.
   The article by P. Politzer et al. is published now, according to the
Springer website
(http://link.springer.de/link/service/journals/00214/tocs.htm, volume 99/2.
You can download it from there if your library has access.) I haven't seen
it in print yet. U. Salzner has a follow-up paper out. It was mentioned in
her comments (J. Phys. Chem. A 1998, 102, 2572)
  In the framework of another project I have looked at DFT-MO energies of
ferrocene, Fe(C5H5)2. (This project was also the motivation for my earlier
CCL question.) Regarding MO energies, we find results that are similar to
the ones published by Salzner et al., in short: Frontier MO energies from
three GGAs are similar. However, hybrid exchange leads to a strong
stabilization of occupied valence MOs;  the virtuals are slightly
destabilized. The HOMO-LUMO gap is almost doubled as a result. I have a
paper submitted to J. Chem. Phys. that contains this stuff.

Best regards, Georg

--
==============================================================
Dr. Georg Schreckenbach           Tel:     (USA)-505-667 7605
Theoretical Chemistry T-12        FAX:     (USA)-505-665 3909
M.S. B268, Los Alamos National      E-mail:  schrecke@t12.lanl.gov
Laboratory, Los Alamos, New Mexico, 87545, USA
Internet:    http://www.t12.lanl.gov/~schrecke/
==============================================================

--Answer from Christopher J. Cramer--
From: cramer@pollux.chem.umn.edu (Christopher Cramer)
Subject: Re: CCL:B3LYP and HF MO differences
To: smori@utsc3.chem.s.u-tokyo.ac.jp (Seiji Mori)
Date: Mon, 27 Apr 1998 10:50:21 -0500 (CDT)

Seiji Mori
>
> Dear netters:
>
>
> I had not posted to CCL for a long time.
>
> By the way, I am now quitely interested in the energy level differences
> between HF and DFT.
>
> Dr. Politzer  said in the summaries
> that they submitted the Theoretical Chemical Account  , but I do not know
> whether this is already published.

Peter Politzer, Fakher Abu-Awwad:
regular article: A comparative analysis of Hartree-Fock and
Kohn-Sham orbital energies
Theor Chem Acc 99 (1998) 2, 83-87

CJC (Associate Editor, TCA)
--

Christopher J. Cramer
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone:  (612) 624-0859 || FAX:  (612) 626-2006
cramer@pollux.chem.umn.edu
http://pollux.chem.umn.edu/~cramer

**************************************************
   Seiji Mori, Ph.D.
  JSPS research fellow
  Lab. of Physical Organic Chemistry, Department of Chemistry
  The University of Tokyo
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  email:smori@utsc3.chem.s.u-tokyo.ac.jp
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  Affilation:
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