From chemistry-request@server.ccl.net  Wed Oct 11 04:10:18 2000
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Reply-To: "Kiniu WONG Kin-Yiu" <kyiwong@phy.cuhk.edu.hk>
From: "Kiniu WONG Kin-Yiu" <kyiwong@phy.cuhk.edu.hk>
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Subject: computation of HOMO-LUMO separation
Date: Wed, 11 Oct 2000 16:10:43 +0800
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Dear all,

    I know there is a CIS option Gaussian to give the excitation energy,
however, this excitation energy involves configuration interactions (CI)
which would destroy the picture of a HOMO-LUMO gap (since in the CI, there
is no more orbitals could be defined).  So, I just want to know the energy
of the dominant (largest coefficient) Slater determinants of CI. Then we
treat it as the HOMO-LUMO gap. But from the Gaussian output, I only see the
coefficient and can't find the energy corresponds to this determinant, for
example:

 CIS wavefunction symmetry could not be determined.
 Eigenvector   1:   ?Spin  -?Sym  Eigenvalue= 0.0000000
      6A ->  8A        -.46865
      6A -> 11A        -.51043
      6A -> 15A        -.10310
      6B ->  8B         .46894
      6B -> 12B         .51278
      6B -> 16B         .10241

So the first question I would want to ask is: How to know the energy
corresponds to each determinant?

    There is a follow-up question.  HF ground energy is just the energy of a
self-consistent Slater determinant involving all occupied (lowest energy)
orbitals.  The second question is: Could Gaussian calculate the energy of a
self-consistent Slater determinant in which some occupied orbitals change to
some virtual orbital?  I know we could change the multiplicity to force one
of electrons to fill a virtual orbital, but could Gaussian do it
arbitrarily?  For example, just see again the above output, could directly
ask Gaussian calculate the energy of a self-consistent Slater determinant in
which 6A changes to 11A?

    Since I am a beginner to Gaussian, any advices are helpful. For example,
is there other softwares could do so? Or are there any literature about
computation of HOMO-LUMO separation?  Thanks in advance!

Regards,
Kiniu

----
Kiniu WONG Kin-Yiu
Undergraduate student
Department of Physics
The Chinese University of Hong Kong
Email: kiniu@cuhk.edu.hk  or  kyiwong@phy.cuhk.edu.hk


From chemistry-request@server.ccl.net  Wed Oct 11 05:02:44 2000
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Good morning from rainy York,

I am looking for a webpage, which compares different quantum mechanic
programs which each other, e.g. what kind of tasks they are able to
fulfill (energy calculations, frequencies, etc.).
Any hints are very welcome,
Meike

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	(message from Chas Simpson on Mon, 9 Oct 2000 11:43:12 +0200 (SAST))
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References:  <Pine.LNX.4.10.10010091037280.22307-100000@sodium.cem.uct.ac.za>

>  correctly.  I heat the system up to 288K from 200K and equilibrate in an
>  NVT ensemlbe at 288K with no problems.  When I try and equilibrate in an
>  NVE ensemble, the temperature jumps to about 350K no matter what I try. (I

You run NVT at 288 K, then switch off the thermostat and get a jump to
350 K?  Assuming that your total energy is constant (easy to verify),
this means that the potential energy must go down significantly.  Look
at some configurations before or after; one of them probably looks
weird. That might help you to find out whether it's the NVT or the NVE
that goes wrong. I don't know how CHARMM does NVT; if there is some
total conserved quantity (e.g. for the Nose-Hoover thermostat), check
that it is indeed conserved.

You might simply be running at the wrong volume - check the pressure,
or, better yet, run NPT dynamics if you can.

   My second question is I am using particle mesh Ewald summations to treat
   the long-range nonbonded interactions. Charmm complains and says that I
   must specify the frequency for stopping the translation and rotation of
   the molecules during the simulation. Why is this necessary and what

You mean translation and rotation of the whole system, right? Not of
the individual molecules, that would make no sense.

In principle, an NVE simulation should keep energy, momentum, and
angular momentum of the system constant. In practice, people get
seriously worried if their energy is not constant (e.g. due to an
excessive integration time step), but accept as inevitable that
momentum and angular momentum are *not* conserved. So if you don't
watch out, all your kinetic energy might be transferred into global
motion, leaving you with what has been described as a "flying ice
cube".

To get rid of this problem, you can remove global motion at regular
intervals and redistribute its kinetic energy to the internal degrees
of freedom. Which, of course, is an unphysical change of your system.
It's a matter of preference how frequently you should do it. You can
argue that it should be done often to make it a small change, or
rarely in order to keep "pure" dynamics for as long as possible.  Most
of all, you should feel bad doing it because it's an ugly kludge ;-)
--
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
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-------------------------------------------------------------------------------


From chemistry-request@server.ccl.net  Wed Oct 11 05:58:11 2000
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Hi,

Could any one tell me if autodock 3 can use both processors on a dual 
processor machine (intel PC/linux)?

Thank you advance for your information.

Sincerely,

Xiao-Ping Zhang

------------------------------------------------
Xiao-Ping Zhang
Department of Biochemistry
Arrhenius Laboratories of Natural Sciences
Stockholm University
106 91 Stockholm
Sweden

Phone: 46-08-162582 / 162472
Fax:     46-08-153679
e-mail: zhang@biokemi.su.se




From chemistry-request@server.ccl.net  Wed Oct 11 06:47:26 2000
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i am working on the simulation of peptides using insightII v 95.I am
facing two problems:
1.after i cap the protein be it using charges or uncharged the peptide is
losing its partial double bond character
2. i am unable to remove charges from the peptide
pl. write to me as to what is to be done now.i am working on this problem
for 3 weeks but so far could not find any solution.my work has stalled due
to this. kindly tell me a solution.
with regards
manjari                    



From chemistry-request@server.ccl.net  Wed Oct 11 09:18:21 2000
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Subject: 00.11.11 Int COnf Elmntry Processes in Molec-Metal Surface Interctns



                         INTERNATIONAL CONFERENCE ON
          ELEMENTARY PROCESSES IN MOLECULE-METAL SURFACE INTERACTIONS
                      San Juan, Puerto Rico, Nov. 11-15


                        http://web.uprr.pr/icep/main.html


The conference will be held at the hotel San Juan Grand Beach Resort & Casino,
San Juan, Puerto Rico, USA, from Saturday, November  11 to Wednesday, November
15, 2000.  The objective of the meeting is to review the latest and most
significant experimental and theoretical advances in small molecule-metal
surface interaction relevant to fuel cell and metal surface erosion processes.
The scientific program will include invited and contributed oral presentations
and posters.

INVITED SPEAKERS:
     A. B. Anderson (Case Western U.)
     S. Bernasek (Princeton U.)
     E. A. Carter (UCLA)
     C. R. Cabrera (U. of Puerto Rico)
     J. Feliu (U. of Alicante)
     A. Fujishima (U. of Tokyo)
     K. M. Glassford (MSI, Inc.)
     D. W. Goodman (Texas A&M U.)
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     C. Lamy (U. of Poitiers)
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     J. K. Norskov (Tech. U. of Denmark)
     D. R. Salahub (NRC, Canada)
     M. Scheffler (Fritz-Haber Inst., Berlin)
     U. Stimming (TU-Munich)

     A. Wieckowski (U. of Illinois)
     J. T. Yates, Jr. (U. of Pittsburgh)
     F. Zaera (UC-Riverside)

Organizing Committee

Cary F. Chabalowski, Army Research Laboratory (Chairman)
Carlos R. Cabrera, University of Puerto Rico
Margaret M. Hurley, Ohio Supercomputer Center
Yasuyuki Ishikawa, University of Puerto Rico
Jerzy Leszczynski, Jackson State University


Current support: University of Puerto Rico, Army Research Office, Office of
Naval Research, Jackson State University Computational Center for Molecular
Structure and Interactions, Army Research Laboratory, DoD High Performance
Modernization Office.

Contacts:

evelyn@adam.uprr.pr - Conference coordinator
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From chemistry-request@server.ccl.net  Wed Oct 11 09:26:11 2000
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Does anybody try GAUSSIAN-98 under SUSE Linux? I will appreciate
information of any kind.
Thanks. Vladimir
-- 
---------------------------------------------
| Dr. Vladimir Pitchko, Ass.Professor        |
| Concordia University College of Alberta    |
| 7128 Ada Boulevard, Edmonton, AB, T5B 4E4  |
| Canada                                     |
| E-mail: vpitchko@concordia.ab.ca           |
| Office telephone # (780) 479-9352          |
| FAX: (780) 474-1933                        |
|---------------------------------------------


From chemistry-request@server.ccl.net  Wed Oct 11 12:40:27 2000
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Date: Wed, 11 Oct 2000 12:44:53 -0400
From: elewars <elewars@trentu.ca>
Subject: SUMMARY MAX PLANCK
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Wed, 2000 Oct 11

Here is the summary of replies, #1--#8 below,  to my questions.
I thank all who answered, and I wish I could have responded to all
individually.
Apparently h stands for Hilfsgroesse (#5).
I have since learned that Dec 14 may be a more appropriate anniversary
than Oct 19 (see e.g. John Ranck, #4 below).
Strange that few _if any_ books bother to say what h stands for, when it
is one of the basic constants of our universe:  "Father knew, in his own
words, that his discovery of the new natural constant had the same
significance as that of Copernicus", T. S. Kuhn, "Black-Body Radiation
and the Quantum Discontinuity, 1894-1912", University of Chicago Press,
chicago, 1978, page 285.

Thanks again

EL
===

The questions:

Monday, 2000 Oct 2

Hello,

On October 19, 1900, Max Planck discovered the quantum discontinuity of
blackbody radiation and sowed the basis for the calculations we all use.

QUESTIONS:

(1) When was the fundamental constant first denoted _h_?  And why _h_?
What word does h stand for?
(I think in classical physics, too, energy x time is "action", but that
starts with _a_.)

(2) Have there been any announcements of the big celebrations that must
surely be planned for the work that marked the transition from classical

to modern physics, revolutionized much of science, and laid the
foundations of new industries?

thanks

E. Lewars
===========
the replies:

#1
You might try the history of chemistry list

eric scerri
Eric Scerri ,
Visiting Professor,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri@chem.ucla.edu
---------
#2
ar E.,

1. h is used for action in physics.

2. The more important celebrations seem to have been arranged by
physicists, eg the APS.

Alejandro Pisanty

.  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .
.  .
     Dr. Alejandro Pisanty
UNAM  -  Educacion Abierta y a Distancia
Av. Universidad 3000, 04510 Mexico DF Mexico
Tel. (+52-5) 622-8713, 622-8633 Fax 550-8405
------------
#3
Hello,

my physics text book told me, that this topic was introduced as _quantum

hypothesis_, may be this is responisble for the _h_.

with best regards

Alex
---

Dr. Alexander Hofmann
Institut fuer Angewandte Chemie Berlin-Adlershof e.V.
Richard-Willstaetter-Str. 12

D-12489 Berlin

hofmann@aca-berlin.de

Tel.: +49-30-6392-4408
Fax.: +49-30-6392-4350

http://www.aca-berlin.de
---------------
#4
Actually, Planck presented his formula for the radiation density "On
an Improvement of Wien's Radiation Law" on October 19.  This was
simply a formula for interpolation between Wien's and Rayleigh's
radiation laws and had (at that time) no theoretical foundations.

He laid out the theoretical foundations for the radiation law
(including his restatement of Boltzmann's entropy as S = k ln W and
the necessity of the quantum of energy) in the paper "On the Theory of
the Energy Distribution Law in the Normal Spectrum" which he presented
to the German Physical Society on December 14, 1900.

It is ironic that Planck was the first to use the constant k which now
carries Boltzmann's name.

> (1) When was the fundamental constant first denoted _h_?  And why
_h_?
> What word does h stand for?
> (I think in classical physics, too, energy x time is "action", but
that
> starts with _a_.)

This doesn't directly answer the above question and it was written
long afterward, but in 1958, Planck wrote (in "Physikalische
Abhandlungen und Vortra(umlaut)ge, Vol1, p. 700):  "Now we have to
consider the distribution of energy E_N [read E sub N] among the N
resonators of frequency (nu).  If E_N were regarded as an infinitely
divisible quantity, the distribution could be performed in an infinite
number of ways.  We consider, however -- and this is the essential
point of the whole computation -- E_N as composed of a finite number
of discrete equal parts and employ for this purpose the natural
constant h = 6.65 x 10^-27 erg sec. This constant multiplied by the
common frequency (nu) of the resonators gives the energy element
(epsilon) in ergs, and by dividing E_N by (epsilon) we obtain the
number P of energy elements which are distributed among the
resonators."

In a letter to Robert Wood in 1931, Planck wrote: " [the ultraviolet
catastrophe] ... can be prevented by assuming that energy is forced,
at the outset, to remain together in certain quanta.  This was purely
a formal assumption and I really did not give it much thought except
that, noo matter what the cost, I must bring about a positive result."

Sorry, I don't immediately have my hands on more of the original
sources.

On with the celebration, but I think December 14 is the date we ought
to memorialize.

John P. Ranck
Elizabethtown College
Elizabethtown, PA 17022
------------------
#5

       "Christoph, van Wuellen,C 3,27870"
<Christoph.vanWullen@TU-Berlin.DE>

As far as I recall, Planck himself introduced "h". It stands for
"Hilfsgroesse", german for "auxiliary quantity".

C.v.W.
----------
#6

>Date: Tue, 03 Oct 2000 10:24:20 -0700
>From: Karl Scherer <scherer@gene.com>
>Reply-To: scherer@gene.com
>Organization: Genentech, Inc.
>X-Sender: "Karl Scherer" <scherer@dna-mail4.gene.com>
>X-Accept-Language: en
>MIME-Version: 1.0
>To: R <rwisniewski@mail.arc.nasa.gov>
>Subject: Re: CCL:MAX PLANCK, QUANTUM THEORY
>
>maybe it derives from german 'Hohlraum' (~black body)? Black body
>radiation was what initially led him to the discovery of the constant.
>
>Karl
>R wrote:
>>
>> >Date: Mon, 02 Oct 2000 19:18:47 -0400
>> >From: elewars <elewars@trentu.ca>
>> >Subject: CCL:MAX PLANCK, QUANTUM THEORY
>> >To: chemistry@ccl.net
>> >MIME-version: 1.0
>> >X-Accept-Language: en
>> >Sender: "Computational Chemistry List" <chemistry-request@ccl.net>
>> >Precedence: bulk
>> >
>> >Monday, 2000 Oct 2
>> >
>> >Hello,
>> >
>> >On October 19, 1900, Max Planck discovered the quantum discontinuity
of
>> >blackbody radiation and sowed the basis for the calculations we all
use.
>> >
>> >QUESTIONS:
>> >
>> >(1) When was the fundamental constant first denoted _h_?  And why
_h_?
>> >What word does h stand for?
>> >(I think in classical physics, too, energy x time is "action", but
that
>> >starts with _a_.)
>> >
>> >(2) Have there been any announcements of the big celebrations that
must
>> >surely be planned for the work that marked the transition from
classical
>> >to modern physics, revolutionized much of science, and laid the
>> >foundations of new industries?
>> >
>> >thanks
>> >
>> >E. Lewars
>> >====

-------------
#7

         "Elizabeth A. Abbott" <eaabbott@att.net>

Hi Dr. Lewars,

I don't know the answer to the 'etymology' of Planck's constant, but I'm

interested!  I checked my textbooks and note that Bohm's _Quantum
Theory_
states Wien's law (on p. 6) as

U(nu)d nu = nu ^3 exp(- h nu / kappa T) d nu

where kappa is Boltzmann's constant and h is Planck's constant.

Then there is a footnote which says, "Wien did not actually introduce
Planck's constant, h, but instead a constant of the form h/kappa (where
kappa is Boltzmann's constant)."  It's not clear to me exactly what
Wien's
formulation was, then.  Perhaps Planck's choice of h was influenced by
Wien's choice of h/kappa.  Wien used thermodynamic arguments to arrive
at
his law, so perhaps his choice of h is thermodynamically informed.

Or maybe h comes from 'harmonic' oscillator??  That seems unlikely,
since
the oscillator is not required to be harmonic.

Verha"ltnis is German for proportion or ratio.  That's just a wild stab
in
the dark.

Hope this trivia is not useless,
Liz
(just a lowly student!)
---------
#8
Huub van Dam                               E-mail: h.j.j.vandam@dl.ac.uk

CCLRC Daresbury Laboratory                  phone: +44-1925-603362
Daresbury, Warrington                         fax: +44-1925-603634
Cheshire, UK
WA4 4AD


Not as far as I know. I haven't even heard of anything to commemorate
the 75th
anniversary of the Schroedinger equation next year...

Huub
================
=============











From chemistry-request@server.ccl.net  Wed Oct 11 20:24:08 2000
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Message-ID: <013201c033e3$8b70eb80$de0b140a@fudan.edu.cn>
From: "Li Zhenhua" <li_zhenhua@etang.com>
To: "CCL" <chemistry@ccl.net>
Subject: how to get MP2(FC) and MP2(FU) energy in a run
Date: Thu, 12 Oct 2000 08:29:37 +0800

Dear members,
I want calculate core correlation energy in a single MP2(FU) run of
Gaussian. I have checked all the help files and iops but can find any
usefull information. I don't want calculate two energies and make
substraction.
 
Thanks very much.

From chemistry-request@server.ccl.net  Wed Oct 11 22:42:12 2000
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Date: Thu, 12 Oct 2000 11:49:23 +0900
To: chemistry@ccl.net
From: ep7@dent.okayama-u.ac.jp (Masao Masamura)
Subject: MC and MD
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Dear Sir:

        I would like to ask you about (1) recent books for Monte Carlo
Simulation and (2) recent books and reviews for constructing an
intermolecular potential for MD and MC.

        Thank you

        M. Masamura


