From chemistry-request@server.ccl.net  Fri Apr 23 02:41:38 1999
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To: chemistry@www.ccl.net
Subject: Re: CCL:screened (Yukawa type) Coulomb potential 
In-reply-to: Your message of "Sun, 18 Apr 1999 17:27:59 JST."
             <199904180828.RAA18624@ashura.qcl01.qcl.t.u-tokyo.ac.jp> 
Date: Fri, 23 Apr 1999 15:37:46 +0900
From: AKINAGA Yoshinobu <akinaga@qcl.t.u-tokyo.ac.jp>

Dear all, 

Some days ago I posted question regarding the evaluation of 
molecular integral with Yukawa type Coulomb potential. 
Following is the reply from Dr. Ugalde, whose work is similar 
to mine and helped me greatly. 
Many thanks.

===============================================================
Akinaga Yoshinobu
Department of Applied Chemistry, Graduate School of Engineering,
University of Tokyo,
Tokyo 113-8656, Japan
tel : 03-3812-2111(7252),  E-mail : akinaga@qcl.t.u-tokyo.ac.jp
===============================================================


> Dear Yoshinobu,
> 
> I have seen your recent message in CCL concerning with the formulation
> of the SCF equations with the Yukawa potential. Indeed, we have solved
> and implemented it as part of the GAMESS program for generalized
> cartesian gaussian basis set functions. I can send you some reprints of
> our published paper. Just drop a note indicating so, or alternatively,
> take a look at our web site.
> 
> To be specific, the integral that you are interested in can be solved
> analytically. Just take a look at our paper,
> 
> Evaluation of the Screened Nuclear Attraction and Electron Repulsion
> Molecular Integrals over Gaussian Basis Functions,
> Jesus M. Ugalde and Cecilia Sarasola
> International Journal of Quantum Chemistry, 62, 273-278 (1997)
> 
> 
> --
> Dr. Jesus M. Ugalde
> Kimika Fakultatea
> Euskal Herriko Unibertsitatea
> P.K.1072
> 20080 Donostia; Euskadi (Spain)
> 
> Voice : +34-943-448190
> Fax   : +34-943-212236
> E-mail: Ugalde@sq.ehu.es
> http://www.sc.ehu.es/chemistry/theory
From chemistry-request@server.ccl.net  Fri Apr 23 08:54:23 1999
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Date: Fri, 23 Apr 1999 14:48:25 +0200 (MESZ)
From: Guenter Kaeb  <gkaeb@ct2.mpibpc.gwdg.de>
Message-Id: <199904231248.OAA10558@ct2.mpibpc.gwdg.de>
To: chemistry@www.ccl.net
Subject: Summary: rare gas vdW interactions
Cc: gkaeb@gwdg.de
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Dear CCLers,

Three weeks ago a posted a message asking for recent work or reviews
on the representation of rare gas vdW interactions.
Here is a summary of the responses I got.

Sincere thanks to Artem Masunov and Sarandis Marinakis!!!

Best, Guenter

---Artem Masunov wrote (April 1, 1999)---
The best analytical fit for Xe...Xe known to me has 14 parameters:
Molecular Physics (1986) 57, 825
and for Ar...Ar and Kr...Kr
R.A.Aziz, M.J.Slaman; Molecular Physics (1986) 58 (4) 679-697

Please summarize.
Best,
Artem

---Sarandis Marinakis wrote (April 1, 1999)---
Dear Dr. Guenter Kaeb,
there are many sources about Xe potential.
1)In Molecular theory of gases,Hirscfelder et al
p.154
2)JCP 1990,V.93,P.7125,Morse Potentail(?)
3)20/6/1991 V.73,N.3,P.471
  20/6/1991 V.73,N.3,P.483
by Pas and Zwolinski.They use 12-6 L-J
(0.3924,257.4) for e and s respectively.
4)JPC 1993,97,7660
5)JCP 1964,41,429
6)J.PHYS.CHEM.REF.DATA,V.3,N.4,1974,979 and many others.
I hope that these will help you.
Respectfully yours,
Sarandis G. Marinakis

---Sarandis Marinakis wrote (April 11, 1999)---
Dear Dr. Guenter Kaeb,
I forgot the following article:
"energy transfer in Ne and Xe collisions
with CO2 at 1eV"
CHEMICAL PHYSICS LETTERS, VOLUME 117,No.2,145-150
(1985).
I hope it is not too late ...
Respectfully yours,
Sarandis G. Marinakis

==============================================================================
=                                                                            =
=  Dr. Guenter Kaeb                                                          =
=  Max-Planck-Institute of Biophysical Chemistry                             =
=  (Department 010: Spectroscopy and photochemical kinetics)                 =
=  Am Fassberg 11                                                            =
=  D-37077 Goettingen                                                        =
=                                                                            =
=  Tel.: +49-551/201-1344                                                    =
=  Fax:  +49-551/201-1006                                                    =
=                                                                            =
=  e-mail: gkaeb@gwdg.de                                                     =
=                                                                            =
==============================================================================
From chemistry-request@server.ccl.net  Fri Apr 23 09:35:08 1999
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Date: Fri, 23 Apr 1999 15:30:02 +0200 (MESZ)
From: Guenter Kaeb  <gkaeb@ct2.mpibpc.gwdg.de>
Message-Id: <199904231330.PAA03960@ct2.mpibpc.gwdg.de>
To: chemistry@www.ccl.net
Subject: Summary: flexible MD code
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Dear CCLers,

On April 13 I posted a message asking for flexible MD codes or bunch of
routines allowing for (relatively) easy implementation of non-standard
and especially complicated interaction potentials. The aim is to study
in detail the energy exchange between vibrational modes of solutes in liquids
and the dissipative loss of vibrational energy to the solvent.
Here is a summary of the responses (more than I expected!!!).

Sincere thanks to all who responded!! I appreciate your hints.

Kind regards, Guenter Kaeb gkaeb@gwdg.de


--- David van der Spoel wrote (April 14, 1999) ---

Hi,

The GROMACS code from the Berendsen group
is quite easily extensible as long as you stick to pair
potentials, and bonded terms. It includes tabulated potentials for
nonbonded interactions, which you
can quite easy extend with your own potential form. It is written in C
with some innerloops (optional) in F77 for performance.

http://md.chem.rug.nl/~gmx

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel         Biomedical center, Dept. of Biochemistry
s-mail: Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: spoel@xray.bmc.uu.se    www: http://zorn.bmc.uu.se/~spoel
phone:  46 18 471 4205          fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


--- Luiz Freitas wrote (April 14, 1999) ---

Dear Guenter,

I am using the tinker package and I found it fine
and easy to use. The has a lot of facilities.
You can get it from

http://dasher.wustl.edu/tinker

Take care
Luiz C G Freitas

--------------------------------------------------
Dr. Luiz Carlos Gomide Freitas
Present address:
Department of Biochemistry and Biophysical Science
University of Houston
Houston, TX 77204-5513, USA

Permanent address:
Laboratorio de Quimica Teorica
Departamento de Quimica
Universidade Federal de Sao Carlos
CP 676
13.565-905 Sao Carlos, SP
Brasil


--- Ferenc Molnar wrote (April 15, 1999) ---
Dear Guenter:

During my PhD thesis I have developed a MD code which "exactly"
does what what you want. I used the code to determine the site
geometries of (small) molecules in rare gas matrices. The code
is written in FORTRAN77 and C and was tested on CRAY, SGI, and
Linux platforms. Currently I am not working very much on the
code which is very flexible in terms of potential surfaces,
but you can contact Dominik Horinek, who continued my work
in Regensburg (Dominik.Horinek@chemie.uni-regensburg.de).
He used the program for OClO, with high quality ab initio data
as a basis for the potentials - this seems to be very close
to what you intend to do.

If you are interested in the Software, feel free to contact either
Dominik or Prof. B. Dick (Bermhard.Dick@chemie.uni-regensburg.de).

Hope this helps!

Ferenc

Ferenc Molnar

----------------------------------------------
Theoretical Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Avenue

Urbana, IL, 61801, USA
Telephone (217) 244-1855
Telefax (217) 244-6078

e-mail ferenc@ks.uiuc.edu
http://www.ks.uiuc.edu/~ferenc

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


--- Vladimir Murashov wrote (April 15, 1999) ---

Hi Guenter,

MolDy codes (in C) could be relatively easily adjusted for
another form of potential interaction.
This classical MD program can be found at
its author web-site
"http://www.earth.ox.ac.uk/~keith/moldy.html"

Regards,
Vladimir V. Murashov, PhD

Dept. Chemistry, University of British Columbia
Vancouver, BC V6T1Z1, Canada


--- Don Steiger wrote (April 15, 1999) ---
Have you looked at

http://www.ks.uiuc.edu/Development/


http://tincan.bioc.columbia.edu/pmd/.


--- Artem Masunov wrote (April 15, 1999) ---

Take a look at TINKER, it has MD and easy to modify.
I'll appreciate your summary.

Artem


>      __   _________  Artem.Masunov@usa.net;tel 212-772-5751;fax 212-772-5332
>     /  \ /  _   _  \ text pager: instantmessage@bigfoot.com (max. 120 char.)
>    /    \\  \\  \\  \  Chemistry Department, Hunter College, City U. of NY
>   /  /\  \\  \\  \\  \      695 Park Avenue, New York, NY 10021
>  /  ____  \\  \\  \\  \  ---------------------------------------------------
> /__/\__/\__\\__\\__\\__\ The early bird may get the worm,
> \__\/  \/__//__//__//__/ but the second mouse gets the cheese.


--- Konrad Hinsen wrote (April 16, 1999) ---

Ich kann meine Simulationsbibliothek MMTK anbieten
(http://starship.python.net/crew/hinsen/mmtk.html, Testversion der
bald erscheinenden stark erweiterten zweiten Version auf
ftp://dirac.cnrs-orleans.fr/pub/ftp). Darin sind zwar keine derartig
genauen Potentiale enthalten, aber die Bibliothek ist so modular, dass
man neue Potentiale einbauen kann, ohne irgendetwas am bestehenden
Code zu aendern.

MfG Konrad Hinsen.
--
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
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From chemistry-request@server.ccl.net  Fri Apr 23 13:50:05 1999
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Date: Fri, 23 Apr 1999 19:45:53 +0200 (MET DST)
From: Pablo Vitoria Garcia <qibvigap@lg.ehu.es>
To: chemistry@ccl.net
Subject: Trouble in G94 with MP2 Freq
Message-ID: <Pine.OSF.3.96.990423194055.3757A-100000@lgdx04.lg.ehu.es>
MIME-Version: 1.0
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Hi all,

This is the first time I tried to calculate the IR spectrum with MP2, and
I have the following problem. I read in the manual that analytical
frequencies need MP2=SEMIDIRECT. So I used the following input:

 %Mem=14MW
 %Chk=/temporal/qipguloj/ptcno4.chk
 #P MP2=(SEMIDIRECT,VERYSTINGY)/LANL2DZ GUESS=READ MAXDISK=1100MB FREQ=
 (ANALYTIC,HPMODES) GEOM=CHECKPOINT

  (rest omitted)

And the computation stopped with:

 Analytic MP2 frequencies require a (semi-)direct transformation.
 Error termination via Lnk1e in /usr/local/g94/l1.exe.
 Job cpu time:  0 days  0 hours  0 minutes  0.4 seconds.

I would appreciate any help. Could it be that analytical frequencies are
not available with core potentials (LANL2DZ is an only-valence basis set,
with core replaced by an ECP).

Thank you very much

Pablo

--------------------------------------------------------------------------------
Pablo Vitoria Garcia 
Departamento de Quimica Inorganica, Facultad de Ciencias
Universidad del Pais Vasco (UPV/EHU)
Apartado 644, E-48080 Bilbao
SPAIN
e-mail: qibvigap@lg.ehu.es
Phone: +34 94 6012000 Ext. 5529
--------------------------------------------------------------------------------

From chemistry-request@server.ccl.net  Fri Apr 23 14:38:54 1999
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Date: Fri, 23 Apr 1999 20:31:14 +0100 (WETDST)
From: Jose Manuel Martinez Fernandez <josema@us.es>
To: chemistry@ccl.net
Subject: oligonucleotide strands MD simulations
Message-Id: <Pine.HPP.3.91.990423202627.19572A-100000@mozart.us.es>
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Dear Netters,
I'm recently involved in MD simulations of nucleotide strands.
I would appreciate any reference concerning free MD simulation 
codes containing a force field library appropiate for DNA simulations.

thanks in advance,
josema



           __________________________________________________________
           _                                                        _
	   _     Jose Manuel Martinez Fernandez, Ph.D.              _
	   _  	Dept. de Quimica Fisica, Universidad de Sevilla     _
	   _  	Facultad de Quimica, SEVILLA 41012, SPAIN           _
	   _     e-mail:  jmmartin@cica.es                          _
	   _              josema@mozart.us.es                       _
           __________________________________________________________


            


From chemistry-request@server.ccl.net  Fri Apr 23 16:49:56 1999
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Date: Fri, 23 Apr 1999 13:43:57 -0700
To: "Merethe Sjovoll" <msj@fskru5.hre.hydro.com>,
        chemistry@www.ccl.net
From: Noppawan Tanpipat <nxt@msi.com>
Subject: Re: CCL:Estimation of vapour pressure of organic liquids and
  solids
Cc: arichards@msicam.co.uk
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Dear Merethe,

MSI has a COSMO-RS feature in the DMol3 program that will predict the
vapour pressure of organic liquids.  For more information see
http://www.msi.com/solutions/products/cerius2/modules/dmol/cosmors.html

Best regards,

Noppawan Tanpipat



At 10:14 AM 4/22/99 -0600, Merethe Sjovoll wrote:
>Hi everybody,
>
>is there a way of estimating in a crude way the vapour pressure of organic
>liquids and solids? I have a whole bunch of molecules and I don't need
absolute
>values, just look for tendencies. So I imagine some calculation formula which
>perhaps contains temperature, possibly boiling point and melting point, or
>perhaps dipole moment, molecular weight etc. (easily accessible quanities).
>
>Is this wishful thinking?
>
>Best regards
>
>Merethe Sjovoll
>
>-- 
>
>********************************************************
>Merethe Sjovoll, Ph.D.                      *          *
>Senior Research Scientist                   *          *
>Norsk Hydro a.s Research Center             *          * 
>                                            *          *
>P.O.Box 2560                                *  HYDRO   *
>N-3907 Porsgrunn,                           * RESEARCH *  
>Norway                                      *          *
>                                            *   (((    *
>email: Merethe.Sjovoll@hre.hydro.com        * (=====)  *
>Phone:+47 35 56 48 97                       *          *
>Fax  :+47 35 56 27 22                       *          *    
>********************************************************
>-= This is automatically added to each message by mailing script =-
>CHEMISTRY@ccl.net -- To Everybody    |   CHEMISTRY-REQUEST@ccl.net -- To
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>MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
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>Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net
>
>
>
>
>
>
>

*************************************
Noppawan Tanpipat, Ph.D.
Product Manager, Quantum Chemistry
Molecular Simulations Inc.
9685 Scranton Road
San Diego, CA 92121

Tel: (619) 799-5332
Fax: (619) 458-0136
Email: nxt@msi.com
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Date: Fri, 23 Apr 1999 17:30:12 -0400 (EDT)
From: "Mildred R. Green PhD" <mildred@houdini.tds-tds.com>
To: Noppawan Tanpipat <nxt@msi.com>
cc: Merethe Sjovoll <msj@fskru5.hre.hydro.com>, chemistry@www.ccl.net,
        arichards@msicam.co.uk
Subject: Re: CCL:Estimation of vapour pressure of organic liquids and  solids
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The  LOADER for Windows program can generate a complete set of
thermodynamically consistent properties for fluids.  The update scheduled
for release in September will also handle the properties of solids.  A
wide variety of estimation methods, including UNIFAC, are available.  More
information about LOADER is available from our WEb site: www.tds-tds.com.

Mildred Green 

------------------------------------------------------------------------------
Technical Database Services, Inc (TDS)     EMAIL: mrgreen@tds-tds.com
Phone:	 212 245 0044
FAX:	 212 247 0587			   WEBSITE: http://www.tds-tds.com
------------------------------------------------------------------------------	

On Fri, 23 Apr 1999, Noppawan Tanpipat wrote:

> 
> Dear Merethe,
> 
> MSI has a COSMO-RS feature in the DMol3 program that will predict the
> vapour pressure of organic liquids.  For more information see
> http://www.msi.com/solutions/products/cerius2/modules/dmol/cosmors.html
> 
> Best regards,
> 
> Noppawan Tanpipat
> 
> 
> 
> At 10:14 AM 4/22/99 -0600, Merethe Sjovoll wrote:
> >Hi everybody,
> >
> >is there a way of estimating in a crude way the vapour pressure of organic
> >liquids and solids? I have a whole bunch of molecules and I don't need
> absolute
> >values, just look for tendencies. So I imagine some calculation formula which
> >perhaps contains temperature, possibly boiling point and melting point, or
> >perhaps dipole moment, molecular weight etc. (easily accessible quanities).
> >
> >Is this wishful thinking?
> >
> >Best regards
> >
> >Merethe Sjovoll
> >
> >-- 
> >
> >********************************************************
> >Merethe Sjovoll, Ph.D.                      *          *
> >Senior Research Scientist                   *          *
> >Norsk Hydro a.s Research Center             *          * 
> >                                            *          *
> >P.O.Box 2560                                *  HYDRO   *
> >N-3907 Porsgrunn,                           * RESEARCH *  
> >Norway                                      *          *
> >                                            *   (((    *
> >email: Merethe.Sjovoll@hre.hydro.com        * (=====)  *
> >Phone:+47 35 56 48 97                       *          *
> >Fax  :+47 35 56 27 22                       *          *    
> >********************************************************
> >-= This is automatically added to each message by mailing script =-
> >CHEMISTRY@ccl.net -- To Everybody    |   CHEMISTRY-REQUEST@ccl.net -- To
> Admins
> >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
> >CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: gopher.ccl.net 70
> >Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net
> >
> >
> >
> >
> >
> >
> >
> 
> *************************************
> Noppawan Tanpipat, Ph.D.
> Product Manager, Quantum Chemistry
> Molecular Simulations Inc.
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From chemistry-request@server.ccl.net  Fri Apr 23 18:23:25 1999
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Date: Fri, 23 Apr 1999 18:18:10 -0400 (EDT)
From: Artem Masunov <amasunov@broadway.GC.cuny.edu>
X-Sender: amasunov@broadway.gc.cuny.edu
To: Merethe Sjovoll <msj@fskru5.hre.HYDRO.com>
Cc: chemistry@www.ccl.net, arichards@msicam.co.uk
Subject: Re: CCL:Estimation of vapour pressure of organic liquids and  solids
In-Reply-To: <Pine.OSF.3.95.990423172523.29726H-100000@houdini.tds-tds.com>
Message-Id: <Pine.OSF.3.93.990423181029.25511B-100000@broadway.gc.cuny.edu>
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Content-Type: TEXT/PLAIN; charset=US-ASCII

 ACD has a module for empirical prediction of vapor pressure.
And it looks to be able to handle solids already.. 

http://www.acdlabs.com/products/bp/

 Hope this helps,

Artem Masunov

On Fri, 23 Apr 1999, Mildred R. Green PhD wrote:

> The  LOADER for Windows program can generate a complete set of
> thermodynamically consistent properties for fluids.  The update scheduled
> for release in September will also handle the properties of solids.  A
> wide variety of estimation methods, including UNIFAC, are available.  More
> information about LOADER is available from our WEb site: www.tds-tds.com.
> ------------------------------------------------------------------------------
> On Fri, 23 Apr 1999, Noppawan Tanpipat wrote:
> > 
> > MSI has a COSMO-RS feature in the DMol3 program that will predict the
> > vapour pressure of organic liquids.  For more information see
> > http://www.msi.com/solutions/products/cerius2/modules/dmol/cosmors.html
> ------------------------------------------------------------------------------
> > >Hi everybody,
> > >
> > >is there a way of estimating in a crude way the vapour pressure of organic
> > >liquids and solids? I have a whole bunch of molecules and I don't need
> > absolute
> > >values, just look for tendencies. So I imagine some calculation formula which
> > >perhaps contains temperature, possibly boiling point and melting point, or
> > >perhaps dipole moment, molecular weight etc. (easily accessible quanities).
> > >
> > >Is this wishful thinking?
> > >
> > >Best regards
> > >
> > >Merethe Sjovoll

