From chemistry-request@server.ccl.net Sun Oct 14 18:09:31 2001
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Date: Mon, 15 Oct 2001 06:09:30 +0800 (CST)
From: =?gb2312?q?WANG=20Xiang?= <xwang90@yahoo.com.cn>
Subject: EVB
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Hi, Dear CCLers:

Does anyone know if the empirical valence bond (EVB)
approach developed by Warshel has been integrated to
CHARMM or not?

Thanks in advance,

Wang, X.


_________________________________________________________
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From chemistry-request@server.ccl.net Mon Oct 15 00:39:25 2001
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Date: Sun, 14 Oct 2001 20:43:49 +0800
From: Denny <dilys98@mails.tsinghua.edu.cn>
To: "chemistry@ccl.net" <chemistry@ccl.net>
Subject: Rwf file 2GB problem again
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Hi CCListers,

I use Gaussian 98 A7 for linux version Redhat 7.0. I am doing a calculation, the input file is: 

%Mem=1800MB
%Rwf=a,250MW,b,250MW,c,250MW,d,250MW,e,250MW,f,250MW,g,250MW,h,250MW,i,250MW,j,-1
%Nosave
%Chk=qtscanf
#T QCISD(T,MaxCyc=5000)/Gen scf(Vshift=100,MaxCycle=2047,symm) Pseudo=Read 
# guess=alter Tran=Direct scan Test

because of the famous 2GB problem, I split .rwf file into many files which are smaller than 2GB. But if I mant to split it 
into more files, the "%Rwf=..." line will be too long and g98 will ignore the extra words. How I can get more disk 
amount(10*250MW) since I can't finish this calculation because the Rwf file here need more than 10*250MW?

Any good advice will be appreciated! 

Best Regards,
Denny Chen

****************************
* Denny Chen		   *
* Center for Astrophysics  *
* Tsinghua University	   *
* Beijing, P.R.China       *
* 8610-62792126(phone)     *
* 8610-62792125(fax)       *
****************************
Email:dilys98@mails.tsinghua.edu.cn



From chemistry-request@server.ccl.net Mon Oct 15 02:42:49 2001
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References: <001201c153cf$2b88b600$3eda623e@mircomputer>
Date: Mon, 15 Oct 2001 08:42:43 +0200
To: "Mirco Meniconi" <mirco.me@tiscalinet.it>
From: Marcel Swart <m.swart@chem.rug.nl>
Subject: Re: CCL:molecular dynamic: wich program?
Cc: CHEMISTRY@ccl.net
Content-Type: multipart/alternative; boundary="============_-1208994328==_ma============"

--============_-1208994328==_ma============
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

>Hi all,
>I'm looking for a free program for bio-molecular dynamics 
>simulations, capable to run under a multiprocessor system.
>could you send me the web-addres where I can find out this program?
>thanks for yours help. 
>--
>Dr. Mirco Meniconi
>university of Perugia (ITALY)
>
>e-mail: <mailto:mirco.me@inwind.it>mirco.me@inwind.it
>phone +39 75 5855114
>mobile +39 328 9526589

See: http://www.gromacs.org

--============_-1208994328==_ma============
Content-Type: text/html; charset="us-ascii"

<!doctype html public "-//W3C//DTD W3 HTML//EN">
<html><head><style type="text/css"><!--
blockquote, dl, ul, ol, li { margin-top: 0 ; margin-bottom: 0 }
 --></style><title>Re: CCL:molecular dynamic: wich
program?</title></head><body>
<blockquote type="cite" cite><font face="Arial" size="-1">Hi
all,</font></blockquote>
<blockquote type="cite" cite><font face="Arial" size="-1">I'm looking
for a free program&nbsp;for bio-molecular dynamics simulations,
capable to run&nbsp;under&nbsp;a multiprocessor
system.</font></blockquote>
<blockquote type="cite" cite><font face="Arial" size="-1">could
you&nbsp;send me the web-addres where&nbsp;I can find out this
program?</font></blockquote>
<blockquote type="cite" cite><font face="Arial" size="-1">thanks for
yours help.&nbsp;</font></blockquote>
<blockquote type="cite" cite><font face="Arial" size="-1">--<br>
Dr. Mirco Meniconi<br>
university of Perugia (ITALY)</font></blockquote>
<blockquote type="cite" cite>&nbsp;</blockquote>
<blockquote type="cite" cite><font face="Arial"
size="-1">e-mail:</font> <a href="mailto:mirco.me@inwind.it"><font
face="Arial" size="-1">mirco.me@inwind.it</font></a><font
face="Arial" size="-1"><br>
phone +39 75 5855114<br>
mobile +39 328 9526589</font></blockquote>
<div><br></div>
<div>See: http://www.gromacs.org</div>
<div><br></div>
</body>
</html>
--============_-1208994328==_ma============--

From chemistry-request@server.ccl.net Mon Oct 15 03:41:07 2001
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  Mon, 15 Oct 2001 09:41:01 +0200
Subject: summary: TDDFT - MO's
To: chemistry@ccl.net
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Dear CCL'ers,

as promised I will give a summary of the comments I received. From work of
Baerends and Gritsenko
it seems that :" "The Kohn-Sham orbitals are physically
sound and may be expected to be more suitable for use in qualitative
molecular orbital theory than either Hartree-Fock or semiempirical
orbitals". And even the linear combinations of these DFT MO's, which are
needed to describe the electron excitations, are claimed to give quite
good results.
Another suggestion was the use of "Natural Transition Orbitals", i.e., to
diagonalize independeently the sets of occupied and virtual MO's.


______________________________________________________________________________
JENS SPANGET-LARSEN:

I am not quite sure that I really understand your question. What do
you mean by "real AO's"? And do you consider AO's and MO's as basis
functions? - But maybe you will find some answers in the following
publications:

E.J. Baerends, O.V. Gritsenko: "A Quantum Chemical View of Density
Functional Theory", J. Phys. Chem. A 101, 5383-5403 (1997)

R. Stowasser, R. Hoffmann: "What Do the Kohn-Sham Orbitals and
Eigenvalues Mean", J. Am. Chem. Soc. 121, 3414-3420 (1999).

P. Bour: "Configuration interaction with Kohn-Sham orbitals and their
relation to excited electronic states", Chem. Phys. Letters 345,
331-337 (2001)

Baerends and Gritsenko state: "The Kohn-Sham orbitals are physically
sound and may be expected to be more suitable for use in qualitative
molecular orbital theory than either Hartree-Fock or semiempirical
orbitals". This point of view is supported by Stowasser and Hoffmann:
" - these seem to be the orbitals a qualitative, chemical analysis
needs". Bour finds that a ".. Slater determinant with the KS orbitals
is more suitable for construction of electronic states" [than a
Slater determinant based on HF orbitals].

Yours, Jens >--<
_____________________________________________________________________________________
Fedor Goumans:

Dear Mr. Goeller,

The 'physical interpration' of KS-MOs has been much debated indeed. As argued by
Baerends and Gritsenko (J. Phys. Chem. A, 101, 5383), the KS-orbitals may be
even more suitable for qualitave MO theory as they include correlation effects
inherently because the Hamiltonian already incorporates them through the Vxc.
Assuming this being so, the KS-orbital picture should be applicable to TD-DFT as
well.
 From the TD-DFT output it is already apparent that the classical one-orbital
excitation picture is incorrect: the one-electron excitation is not to a pure
virtual orbital but to a state which is a linear combination of those. Analysis
of the photochemistry based on the composition of the KS-orbitals for the
1-electron excitations have been applied in the following articles:
J.Phys.Chem.A, 103, 6835
J.Am.Chem.Soc., 121, 10356
 From the same authors a number of studies using Ziegler's Delta-SCF method for
calculation of the excited state surfaces have also been published.
I hope this helps,
Kind regards,
Fedor Goumans
___________________________________________________________________________
Geoff Hutchison:

> can we then really interpret these orbitals as the ones from and to
> which electrons are excited? Is this model stable and can it be
> interpreted photochemically? I am not aware of any publication dealing
> with this.

Dr. Richard Martin of Los Alamos National Lab gave a talk on this subject
at a conference there this summer. He called these "Natural Transition
Orbitals" and said while he wasn't sure it hadn't already been done, he
was thinking of writing it up.

In short, he defined new orbitals, the occupied orbitals by T(T+) and the
virtual orbitals by (T+)T--diagonalizing each set.

I don't know how good an explanation that is, but it didn't seem to hard
and he seemed willing to share the method.

--
-Geoff Hutchison                <hutchisn@chem.nwu.edu>
Marks/Ratner Groups             (847) 491-3295
Northwestern Chemistry          <http://www.chem.nwu.edu>
___________________________________________________________________________
Stefan Grimme:

Dear Andreas,
If you interpret the KS orbitals as solutions to some
mean-field eigenvalue equation with an effective (XC)-potential
and use them as "MOs" in the usual sense, its also valid
to interpret the "excitations" from TDDFT in the usual manner,
i.e. for bonding/anti-bonding discussions and so on. My main
argument for this is that the TDDFT properties like oscillator
strengths are calculated exactly as in TDHF e.g. by taking
the transition densities and multiply with the one-electron integrals
over the KS orbitals. However, in practice I strongly recommend to
restrict all of these discussions to KS orbitals with negative
eigenvalues (bound one-particle states) because everything else
suffers from the wrong asymtotic behaviour of most functionals used
(take e.g. a Neon atom with a basis set containg a large number of the
proper Rydberg functions and calculated the 2p-ns Rydberg series:
everything except the first one is garbage showing not the correct
series behaviour for e.g. <r>, <r^2> expectation values).
Stefan

Prof. Dr. Stefan Grimme
_______________________________________________________________________________
Hi,

> There is a lot of discussion if the basis set (which even in HF theory is only
a
> model for the real AO's), which
> represents the real electron density of the whole state, can be used for
> interpretation as MO's.

I thought it could NOT

Cordially,
George
_________________________________________________________________________________





From chemistry-request@server.ccl.net Mon Oct 15 08:21:20 2001
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Subject: Re: CCL:Rwf file 2GB problem again
To: chemistry@ccl.net (CCL)
Date: Mon, 15 Oct 2001 13:21:08 +0100 (BST)
In-Reply-To: <200110150439.f9F4dJB22589@server.ccl.net> from "Denny" at Oct 14, 2001 08:43:49 PM
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Hi Denny,

> because of the famous 2GB problem, I split .rwf file into many files which are smaller than 2GB. But if I mant to split it 
> into more files, the "%Rwf=..." line will be too long and g98 will ignore the extra words. How I can get more disk 
> amount(10*250MW) since I can't finish this calculation because the Rwf file here need more than 10*250MW?
> 

I don't think there is an easy way around this for revision A7. One solution 
is to obtain the latest revision, A11, which supports link 0 commands 
(% lines) of up to 500 characters (see www.gaussian.com).

Best wishes,

Tanja 
-- 
  =====================================================================
     Tanja van Mourik                                                
     Royal Society University Research Fellow
     Chemistry Department 
     University College London    phone:    +44 (0)20-7679-4663      
     20 Gordon Street             e-mail:   work: T.vanMourik@ucl.ac.uk 
     London WC1H 0AJ, UK                    home: tanja@netcomuk.co.uk     

     http://www.chem.ucl.ac.uk/people/vanmourik/index.html
  =====================================================================

From chemistry-request@server.ccl.net Mon Oct 15 08:25:02 2001
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Date: Mon, 15 Oct 2001 07:24:53 -0500
To: "Mirco Meniconi" <mirco.me@tiscalinet.it>
From: Robert Brunner <rbrunner@uiuc.edu>
Subject: Re: CCL:molecular dynamic: wich program?
Cc: chemistry@ccl.net, namd@ks.uiuc.edu
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

>Hi all,
>I'm looking for a free program for bio-molecular dynamics 
>simulations, capable to run under a multiprocessor system.
>could you send me the web-addres where I can find out this program?
>thanks for yours help. 
>--
>Dr. Mirco Meniconi
>university of Perugia (ITALY)
>
>e-mail: <mailto:mirco.me@inwind.it>mirco.me@inwind.it
>phone +39 75 5855114
>mobile +39 328 9526589


NAMD is a fast, free parallel MD program. See 
<http://www.ks.uiuc.edu/Research/namd>

Robert




-- 


From chemistry-request@server.ccl.net Mon Oct 15 11:28:14 2001
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From: =?iso-8859-1?Q?Tommi_Nyr=F6nen?= <nyronen@csc.fi>
To: <chemistry@ccl.net>
Subject: combichem for pc
Date: Mon, 15 Oct 2001 18:31:21 +0300
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Dear ccl people,

could somebody recommend a good free/low-cost program for PC (Linux, Win)
for doing combinatorial chemistry?

I searching for a simple program that would be able to add library of
fragments to defined points in a molecule. Program could be 2D, 3D, line
input, graphical user interface etc as long as the program can output SD
files, mol2 files or something else that can be easily read into major
modeling programs.

thanks for any help, I'll summarize

    -tommi-

: Tommi Nyr鰊en, Cheminformatics & Drug discovery
: CSC - Scientific Computing Ltd. Tekniikantie 15 a D 02101 Espoo
: tel. +358-9-4572235 mob. +358-50-3819511 fax. +358-9-4572302



From chemistry-request@server.ccl.net Mon Oct 15 21:13:39 2001
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Reply-To: "Andrew Dalke" <dalke@dalkescientific.com>
From: "Andrew Dalke" <adalke@mindspring.com>
To: <chemistry@ccl.net>
Subject: PyDaylight-0.8 available
Date: Mon, 15 Oct 2001 19:08:23 -0600
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PyDaylight version 0.8 has been released and is available for
download from http://sourceforge.net/projects/pydaylight/ .

New in this release:
  - Project hosting at Sourceforge.net
  - Uses Distutils for easy compilation and installation.
      (Requires Python 2.x)
  - Reaction and SMIRKS support
  - Improved program object support (both client and server)
  - PDF depiction output
  - Bug fixes and performance improvements.


PyDaylight is a Python interface to the Daylight toolkit.  In addition
to low-level bindings to the toolkit functions, it provides a true
object layer, iterators, exceptions and various useful libraries for
chemical informatics.

PyDaylight is freely available under the terms of the GNU LGPL.

For more information, about PyDaylight or to hire Dalke Scientific
Software for consulting based on PyDaylight, please visit

  http://www.dalkescientific.com/PyDaylight/

Many thanks to Bioreason, Daylight, Vertex, and AstraZeneca for their
assistance in developing PyDaylight.

"Daylight" and "Daylight toolkit" are registered trademarks of
Daylight Chemical Information Systems, Inc. Daylight C.I.S. is not
responsible for PyDaylight.

                            Andrew Dalke
                            dalke@dalkescientific.com