From owner-chemistry@ccl.net Thu Jun 18 00:13:01 2009
From: "Leila Ram lram5228 : usyd.edu.au" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: Particle-mesh method
Message-Id: <-39544-090618001107-8495-13oPfKaJfIeO/iTHOycaNQ() server.ccl.net>
X-Original-From: "Leila  Ram" <lram5228-#-usyd.edu.au>
Date: Thu, 18 Jun 2009 00:11:03 -0400


Sent to CCL by: "Leila  Ram" [lram5228]^[usyd.edu.au]
Hi,

for the charge calculation in lubricant system under friction, which method is preffered, Ewald summation or Particle-mesh method(PPPM) and why?
also, Can you please give me some source code(Fortran preffered) for PPPM calculation?
Your advise would be highly appriciated.

Leila


From owner-chemistry@ccl.net Thu Jun 18 06:40:00 2009
From: "Jacopo Sgrignani sgrigna-$-gmail.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: Modeling of Copper
Message-Id: <-39545-090618062826-28813-PQGpG1Rv7ihgw84RWXtJxA++server.ccl.net>
X-Original-From: Jacopo Sgrignani <sgrigna/./gmail.com>
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Date: Thu, 18 Jun 2009 12:28:16 +0200
MIME-Version: 1.0


Sent to CCL by: Jacopo Sgrignani [sgrigna _ gmail.com]
--0015174c18baaf9932046c9cdd3c
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Dear all
could you suggest me, reviews, book chapters or papers about the approaches
to model copper-protein
interaction in classic molecular dynamics.
Thanks in advance

Jacopo

--0015174c18baaf9932046c9cdd3c
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Dear all<br>could you suggest me, reviews, book chapters or papers about the approaches to model copper-protein <br>interaction in classic molecular dynamics.<br>Thanks in advance<br><br>Jacopo<br>

--0015174c18baaf9932046c9cdd3c--


From owner-chemistry@ccl.net Thu Jun 18 07:15:01 2009
From: "Andreas Bick andreas.bick++scienomics.com" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: Particle-mesh method
Message-Id: <-39546-090618065230-2230-toXgN18mhGPQCBNiSUFPKA ~~ server.ccl.net>
X-Original-From: Andreas Bick <andreas.bick**scienomics.com>
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Date: Thu, 18 Jun 2009 12:52:17 +0200
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Sent to CCL by: Andreas Bick [andreas.bick]*[scienomics.com]
Dear Leila,

why do you not try the free LAMMPS code, available at 
http://lammps.sandia.gov/

It contains both methods and is also available as source code.

Best regards

Andreas
> Sent to CCL by: "Leila  Ram" [lram5228]^[usyd.edu.au]
> Hi,
> 
> for the charge calculation in lubricant system under friction, which method is preffered, Ewald summation or Particle-mesh method(PPPM) and why?
> also, Can you please give me some source code(Fortran preffered) for PPPM calculation?
> Your advise would be highly appriciated.
> 
> Leila> 
> 
> 


-- 
Dr. Andreas Bick
Scienomics SARL
Sales and Marketing
mobile: +491621309945


From owner-chemistry@ccl.net Thu Jun 18 07:51:01 2009
From: "selva raj selvacbm a yahoo.co.in" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: dear sir
Message-Id: <-39547-090618072931-24629-ev2HMXo8REvZ2fFoe0GeTw,server.ccl.net>
X-Original-From: "selva  raj" <selvacbm ~~ yahoo.co.in>
Date: Thu, 18 Jun 2009 07:29:27 -0400


Sent to CCL by: "selva  raj" [selvacbm],[yahoo.co.in]
I am doing docking studies please tell me about how do calculate the accessible surface area 

                          THANKING YOU
                          SELVARAJ


From owner-chemistry@ccl.net Thu Jun 18 08:36:01 2009
From: "Michel Petitjean petitjean.chiral(-)gmail.com" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL: Surfaces (was: dear sir)
Message-Id: <-39548-090618083209-18575-3XrYREmOu1szsAGbjUaLAw-.-server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral**gmail.com>
Content-Transfer-Encoding: 7bit
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Date: Thu, 18 Jun 2009 14:24:49 +0200
MIME-Version: 1.0


Sent to CCL by: Michel Petitjean [petitjean.chiral**gmail.com]
Dear Selva Raj,
You can compute surfaces and volume with the ASV freeware
(http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV).
Both the analytical method and the Monte-Carlo computation are included in ASV.
Best regards,

Michel Petitjean,
DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528,
91191 Gif-sur-Yvette Cedex, France.
Phone: +331 6908 4006 / Fax: +331 6908 4007
E-mail: michel.petitjean#,#cea.fr, petitjean.chiral#,#gmail.com
http://petitjeanmichel.free.fr/itoweb.petitjean.html


> From: selva raj selvacbm a yahoo.co.in <owner-chemistry#,#ccl.net>
Date: 2009/6/18
Subject: CCL: dear sir
Sent to CCL by: "selva  raj" [selvacbm],[yahoo.co.in]

I am doing docking studies please tell me about how do calculate the
accessible surface area

                         THANKING YOU
                         SELVARAJ


From owner-chemistry@ccl.net Thu Jun 18 09:11:01 2009
From: "Leonardo Moreira Costa leo.mcosta!=!yahoo.com.br" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: Calculation of the Partition Coeficient
Message-Id: <-39549-090618084640-32268-zfr6i50Ech0EWm5iQn4bbA++server.ccl.net>
X-Original-From: "Leonardo Moreira Costa" <leo.mcosta_-_yahoo.com.br>
Date: Thu, 18 Jun 2009 08:46:36 -0400


Sent to CCL by: "Leonardo Moreira Costa" [leo.mcosta]|[yahoo.com.br]
Hi friends !

I want to know how can I calculate the partition coeficient of a molecule. Does anyone know which program can I use?

Thanks you all
Leo Costa
leo.mcosta:-:yahoo.com.br


From owner-chemistry@ccl.net Thu Jun 18 09:46:00 2009
From: "Pedro Silva pedros]-[ufp.edu.pt" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: Singlet to Multiplet PE Surfaces
Message-Id: <-39550-090617172939-9190-n27gLqdisGfbGe+aPpAM5Q:+:server.ccl.net>
X-Original-From: Pedro Silva <pedros^-^ufp.edu.pt>
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Date: Wed, 17 Jun 2009 22:00:01 +0100
MIME-Version: 1.0


Sent to CCL by: Pedro Silva [pedros/./ufp.edu.pt]
Your reactants are a triplet state. If your product is a also a
triplet state, finding a transition state is strightforward: just
perform a saddle point search using UHF (or UDFT, UMP2, etc.). If your
product is a singlet, you will have to find a minimum-energy crossing
point between the singlet and triplet surfaces and compute the
spin-orbit coupling at that point. Not really a transition point
search, but not an intractable problem. I happen to have done that in
several different systems already, but I learn it from a few papers by
Per Siegbahn.

Pedro Silva

A few references:
Journal of Biological Inorganic Chemistry, 13, 929-940
New J. Chem., 2000, 24, 77 - 80
J. Phys. Chem. B, 112, 3144-3148.
Chemical Physics Letters,  401, Issues 4-6, 347-351
Bioorg. Med. Chem., 16, 2726-2733.
J. Phys. Org. Chem. 2006; 19: 25=9633



On Wed, Jun 17, 2009 at 6:22 PM, Mark Zottola mzottola . gmail.com
<owner-chemistry++ccl.net> wrote:
>
> I need the more robust theoreticians on this list to settle a debate in m=
y lab.
>
> I have a system which is in a singlet spin state.=A0 A colleague wants to=
 calculate the transition state for the oxidation of this system by=A0an ox=
ygen atom.
>
> I have said I do not believe we can do this as bringing 2 molecular speci=
es in the triplet and singlet states would make location of the transition =
state impossible.=A0 The question of multiplicity changeing as the distance=
 between the two species changing is not something quantum mechanics can do=
.=A0 My colleague claims his old group did that type of calculation on a ve=
ry frequent basis.
>
> So my questions are - am I wrong in thinking that the problem, as posed, =
is intractable?=A0 Can you actually quench a spin state in the transition s=
tate?=A0 If there are methods to handle this, would anyone be willing to po=
int me to them?
>
> Thanks!
>
>
> Mark


--
Pedro J. Silva
Assistant Professor
Universidade Fernando Pessoa
Porto - Portugal
http://www2.ufp.pt/~pedros/science/science.htm


From owner-chemistry@ccl.net Thu Jun 18 10:22:00 2009
From: "Joop van Lenthe j.h.vanlenthe_-_uu.nl" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Singlet to Multiplet PE Surfaces
Message-Id: <-39551-090617183151-19569-lBhT2yEEg1DIZLWeRlgp1g^^server.ccl.net>
X-Original-From: Joop van Lenthe <j.h.vanlenthe\a/uu.nl>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Date: Wed, 17 Jun 2009 23:14:20 +0200
Mime-Version: 1.0 (Apple Message framework v935.3)


Sent to CCL by: Joop van Lenthe [j.h.vanlenthe^uu.nl]
In classical quantumchemistry the momentum is conserved, so yes ou  
cannot change the multiplicity.
However this assumes teh Hamiltonian does not contain spin terms.
If it does contain spin orbit terms the spin angular momentum is not a  
constant of motion anymoreand the spinstate may change over a
a potential energy surface.
Spin orbit interaction is included in a few programs; Not only
fully relativistic ones but also including simpler models.
Joop

===============================
Joop van Lenthe
Theoretical Chemistry Group Utrecht
tel. -31-30-2532733
joop++chem.uu.nl
===============================

On 17/06/2009, at 7:22 PM, Mark Zottola mzottola . gmail.com wrote:

> I need the more robust theoreticians on this list to settle a debate  
> in my lab.
>
> I have a system which is in a singlet spin state.  A colleague wants  
> to calculate the transition state for the oxidation of this system  
> by an oxygen atom.
>
> I have said I do not believe we can do this as bringing 2 molecular  
> species in the triplet and singlet states would make location of the  
> transition state impossible.  The question of multiplicity changeing  
> as the distance between the two species changing is not something  
> quantum mechanics can do.  My colleague claims his old group did  
> that type of calculation on a very frequent basis.
>
> So my questions are - am I wrong in thinking that the problem, as  
> posed, is intractable?  Can you actually quench a spin state in the  
> transition state?  If there are methods to handle this, would anyone  
> be willing to point me to them?
>
> Thanks!
>
>
> Mark


From owner-chemistry@ccl.net Thu Jun 18 10:56:00 2009
From: "Andreas Klamt klamt-.-cosmologic.de" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: Calculation of the Partition Coeficient
Message-Id: <-39552-090618095719-5675-IyQ5G8YICWJHSAT//cVxTw[-]server.ccl.net>
X-Original-From: Andreas Klamt <klamt[]cosmologic.de>
Content-Transfer-Encoding: quoted-printable
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Date: Thu, 18 Jun 2009 15:57:09 +0200
MIME-Version: 1.0


Sent to CCL by: Andreas Klamt [klamt[]cosmologic.de]
If you want to calculate an octanol-water partition coefficient at room=20
temperature, there are tons of programs to do so, e.g. CLOGP, LOGKOW,=20
ACD, ...., COSMOtherm

If you are looking for general patition coefficients of solutes between=20
solvent1 and solvent2, where both may even be mixtures, at variable=20
temperature, then most likely the COSMO-RS method as implemented in=20
COSMOtherm is the only practical solution for your request.

Andreas

Leonardo Moreira Costa leo.mcosta!=3D!yahoo.com.br schrieb:
> Sent to CCL by: "Leonardo Moreira Costa" [leo.mcosta]|[yahoo.com.br]
> Hi friends !
>
> I want to know how can I calculate the partition coeficient of a molecu=
le. Does anyone know which program can I use?
>
> Thanks you all
> Leo Costa
> leo.mcosta],[yahoo.com.br
>
>
>
> -=3D This is automatically added to each message by the mailing script =
=3D-
> To recover the email address of the author of the message, please chang=
e>
> Subscribe/Unsubscribe:=20>
> Job: http://www.ccl.net/jobs=20=>
>
>
>
>  =20


--=20
PD. Dr. Andreas Klamt
CEO / Gesch=E4ftsf=FChrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt,+,cosmologic.de
web    	www.cosmologic.de

HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt


From owner-chemistry@ccl.net Thu Jun 18 11:46:00 2009
From: "David Gallagher gallagher.da:+:gmail.com" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: Calculation of the Partition Coeficient
Message-Id: <-39553-090618114005-23811-3pq3f2Yh7sdBPp9bfPdpuw-$-server.ccl.net>
X-Original-From: David Gallagher <gallagher.da]~[gmail.com>
Content-Type: multipart/alternative;
	boundary="=====================_1649140==.ALT"
Date: Thu, 18 Jun 2009 08:12:51 -0700
Mime-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da() gmail.com]
--=====================_1649140==.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed

Hi Leo,

COSMOtherm would be an obvious choice for the liquid phase and it 
also works for ionic liquids.  A related program, COSMOmic, 
calculates partitioning in membranes and micelles.  Both methods are 
based on DFT quantum chemistry and statistical thermodynamics.  There 
is more information and a bibliography at 
<http://cacheresearch.com/cosmo.html>http://cacheresearch.com/cosmo.html

David Gallagher
CACheResearch.com


At 05:46 AM 6/18/2009, Leonardo Moreira Costa leo.mcosta!=!yahoo.com.br wrote:

>Sent to CCL by: "Leonardo Moreira Costa" [leo.mcosta]|[yahoo.com.br]
>Hi friends !
>
>I want to know how can I calculate the partition coeficient of a 
>molecule. Does anyone know which program can I use?
>
>Thanks you all
>Leo Costa
>leo.mcosta],[yahoo.com.br--=====================_1649140==.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<body>
Hi Leo,<br><br>
COSMOtherm would be an obvious choice for the liquid phase and it also
works for ionic liquids.&nbsp; A related program, COSMOmic, calculates
partitioning in membranes and micelles.&nbsp; Both methods are based on
DFT quantum chemistry and statistical thermodynamics.&nbsp; There is more
information and a bibliography at
<a href="http://cacheresearch.com/cosmo.html">
http://cacheresearch.com/cosmo.html</a> <br><br>
David Gallagher<br>
CACheResearch.com<br><br>
<br>
At 05:46 AM 6/18/2009, Leonardo Moreira Costa leo.mcosta!=!yahoo.com.br
wrote:<br><br>
<blockquote type=cite class=cite cite="">Sent to CCL by: &quot;Leonardo
Moreira Costa&quot; [leo.mcosta]|[yahoo.com.br]<br>
Hi friends !<br><br>
I want to know how can I calculate the partition coeficient of a
molecule. Does anyone know which program can I use?<br><br>
Thanks you all<br>
Leo Costa<br>
leo.mcosta],[yahoo.com.br<br><br>
<br><br<br<br<br<br><br<br>
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Before posting, check wait time at:
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From owner-chemistry@ccl.net Thu Jun 18 12:41:00 2009
From: "Brunsteiner, Michael micb|-|uic.edu" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL: Particle-mesh method
Message-Id: <-39554-090618040632-20010-MI9vGdXs0w8o4d06iKnMdA*o*server.ccl.net>
X-Original-From: "Brunsteiner, Michael" <micb|uic.edu>
Content-Transfer-Encoding: 8bit
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Date: Thu, 18 Jun 2009 02:06:23 -0500 (CDT)
MIME-Version: 1.0


Sent to CCL by: "Brunsteiner, Michael" [micb%a%uic.edu]
On Wed, June 17, 2009 23:11, Leila Ram lram5228 : usyd.edu.au wrote:
>
> Sent to CCL by: "Leila  Ram" [lram5228]^[usyd.edu.au]
> Hi,
>
> for the charge calculation in lubricant system under friction, which
> method is preffered, Ewald summation or Particle-mesh method(PPPM) and
> why?

There is number of methods (EW, PME, FMA, PPPM) out there
and a lot of studies have been published discussing the merits
of one or the other, but if properly implemented and
parameterized the performance in terms of accuracy/speed
is probably similar for all of them, unless you have an
exceptionally large system, in which case PPPM or FMA might
be more efficient than an Ewald based method (some people
have claimed). This being said, I assume the system you are
dealing with is anisotropic (i.e. periodic in less than 3
dimensions), and in such a case PPPM might be the better
choice, as accounting for anisotropy with any other method
is comparatively cumbersome IIRC.

Unfortunately there's not much out there in terms of open source
PPPM. The only open source package that I am aware of which
has PPPM implemented is Gromcas, but be warned, the Gromacs
source code is rather involved and complex. If you are not
good at C-programming understanding this code might turn out
to be more time consuming than writing something from scratch.

implementation of any serious method to account for electrostatic
long range interactions is generally a rather non-trivial task.
If your lubricants have a low enough dielectric permittivity you
might get away with some variation of a cut-off based method
which is considerably easier to code (and parallelize).

good luck!
mic


> also, Can you please give me some source code(Fortran preffered)
> for PPPM calculation?
> Your advise would be highly appriciated.
>
> Leila


From owner-chemistry@ccl.net Thu Jun 18 13:15:00 2009
From: "Elaine Meng meng{}cgl.ucsf.edu" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: dear sir (calculating accessible surface areas)
Message-Id: <-39555-090618120111-6801-tz6Za7qc5/cjkIFR/eNj/A{:}server.ccl.net>
X-Original-From: "Elaine  Meng" <meng,+,cgl.ucsf.edu>
Date: Thu, 18 Jun 2009 12:01:08 -0400


Sent to CCL by: "Elaine  Meng" [meng]*[cgl.ucsf.edu]
Hello,
Here are some web servers that can calculate accessible surface areas:

(1) NIH StrucTools server, where the Calculate options include "Accessible surface (Gerstein)" and Output type includes "text", which will give values per atom, per residue, and total:

http://helixweb.nih.gov/structbio/basic.html

(2) GetArea server, where you can choose whether you want values per atom, residue, or total (along with some additional information):

http://curie.utmb.edu/getarea.html

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng^^cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html


From owner-chemistry@ccl.net Thu Jun 18 13:50:00 2009
From: "oscolv]|[yahoo.com.mx" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: Singlet to Multiplet PE Surfaces
Message-Id: <-39556-090618115503-758-IbHNnayGGD5WxZHRsL75lQ[*]server.ccl.net>
X-Original-From: oscolv##yahoo.com.mx
Content-Transfer-Encoding: quoted-printable
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Date: Thu, 18 Jun 2009 07:54:50 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: oscolv**yahoo.com.mx

If necessary to change the multiplicity when you study a PES, for example:=
=0A=0AAu(5d106s1)+NO(2PI)--> AuNO (Singlet)=0A=0AWhen the reactives are ver=
y separate the wavefunction has to describe a triplet, but when the molecul=
es are approaching, the compound formed has multiplicity 1. In order to stu=
dy an interaction like this you need to use a multiconfigurational wavefunc=
tion and take account the electronic correlation energy by theory perturbat=
ion, for example the methods:=0A=0ACASPT2-- MOLCAS program=0AMRPT2-- GAMESS=
 program=0AQDCPT2-- GAMESS program=0A=0AIf you have only one determinant li=
ke HF or DFT you cant obtain a PES in all region, only in the minimum=0A=0A=
=0A=0A--- El mi=E9 17-jun-09, Joop van Lenthe j.h.vanlenthe_-_uu.nl <owner-=
chemistry-.-ccl.net> escribi=F3:=0A=0A> De:: Joop van Lenthe j.h.vanlenthe_-_=
uu.nl <owner-chemistry-.-ccl.net>=0A> Asunto: CCL: Singlet to Multiplet PE Su=
rfaces=0A> A: "Olvera, Oscar " <oscolv-.-yahoo.com.mx>=0A> Fecha: mi=
=E9rcoles 17 de junio de 2009, 16:14=0A> =0A> Sent to CCL by: Joop van Lent=
he [j.h.vanlenthe^uu.nl]=0A> In classical quantumchemistry the momentum is =
conserved, so=0A> yes ou cannot change the multiplicity.=0A> However this a=
ssumes teh Hamiltonian does not contain spin=0A> terms.=0A> If it does cont=
ain spin orbit terms the spin angular=0A> momentum is not a constant of mot=
ion anymoreand the=0A> spinstate may change over a=0A> a potential energy s=
urface.=0A> Spin orbit interaction is included in a few programs; Not=0A> o=
nly=0A> fully relativistic ones but also including simpler models.=0A> Joop=
=0A> =0A> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0A> Joop van Lenthe=0A> Theoretical Chemistr=
y Group Utrecht=0A> tel. -31-30-2532733=0A> joop*chem.uu.nl=0A> =3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=0A> =0A> On 17/06/2009, at 7:22 PM, Mark Zottola mzottola .=0A> g=
mail.com wrote:=0A> =0A> > I need the more robust theoreticians on this lis=
t to=0A> settle a debate in my lab.=0A> > =0A> > I have a system which is i=
n a singlet spin=0A> state.=A0 A colleague wants to calculate the transitio=
n=0A> state for the oxidation of this system by an oxygen atom.=0A> > =0A> =
> I have said I do not believe we can do this as=0A> bringing 2 molecular s=
pecies in the triplet and singlet=0A> states would make location of the tra=
nsition state=0A> impossible.=A0 The question of multiplicity changeing as=
=0A> the distance between the two species changing is not=0A> something qua=
ntum mechanics can do.=A0 My colleague=0A> claims his old group did that ty=
pe of calculation on a very=0A> frequent basis.=0A> > =0A> > So my question=
s are - am I wrong in thinking that the=0A> problem, as posed, is intractab=
le?=A0 Can you actually=0A> quench a spin state in the transition state?=A0=
 If there=0A> are methods to handle this, would anyone be willing to point=
=0A> me to them?=0A> > =0A> > Thanks!=0A> > =0A> > =0A> > Mark=0A> =0A> =0A=
> =0A> -=3D This is automatically added to each message by the=0A> mailing =
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From owner-chemistry@ccl.net Thu Jun 18 14:32:00 2009
From: "Marc Baaden baaden]~[smplinux.de" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: Force field parameters for modeling a Cr2O3 surface ?
Message-Id: <-39557-090618131108-27679-WPWx1/ehrTD+y4VPnCLilQ[*]server.ccl.net>
X-Original-From: "Marc  Baaden" <baaden^-^smplinux.de>
Date: Thu, 18 Jun 2009 13:11:04 -0400


Sent to CCL by: "Marc  Baaden" [baaden%%smplinux.de]
Dear All,

A colleague of mine working on surfaces and adsorption phenomena was asking about (classical) 
simulations of such a surface in contact with water and potentially adsorbing small molecules. The 
targeted surface is Cr2O3.

A quick literature search for either forcefield parameters of such a surface or case studies based on 
classical (eg molecular dynamics) simulations did not reveal any significant hits. Then again, I am 
more specialized in biological molecules, so maybe I just missed the relevant papers.

Any pointers to papers, parameters and shared experience (on successes or failures) would be greatly 
appreciated,

Sincerely,
Marc Baaden
--
http://www.baaden.ibpc.fr/projects/mddriver/
LBT - IBPC - CNRS - Paris


From owner-chemistry@ccl.net Thu Jun 18 15:00:01 2009
From: "Soren Eustis soreneustis(a)gmail.com" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: Strange Behavior with CuCl3 Optimizations
Message-Id: <-39558-090618144444-4034-6gpIHVizq3OVeiXPdN9D2Q,server.ccl.net>
X-Original-From: "Soren  Eustis" <soreneustis/a\gmail.com>
Date: Thu, 18 Jun 2009 14:44:40 -0400


Sent to CCL by: "Soren  Eustis" [soreneustis{}gmail.com]
I am having a real unique issue with CuCl3 optimizations.  I have tried this calculation with both MP2 and DFT and the result is quite similar.  Initially the routine makes one or two moves which lower the energy, then it seems that each successive move actually raises the energy reaching some asymptote.  Here is the result of 20+ iterations:

1	-3021.50722196000
2	-3021.50701328000
3	-3021.50759033000
4	-3021.50698239000
5	-3021.50633890000
6	-3021.50583991000
7	-3021.50549299000
8	-3021.50526333000
9	-3021.50511954000
10	-3021.50502651000
11	-3021.50496526000
12	-3021.50492450000
13	-3021.50489721000
14	-3021.50487884000
15	-3021.50486646000
16	-3021.50485811000
17	-3021.50485245000
18	-3021.50484862000
19	-3021.50484603000
20	-3021.50484427000
21	-3021.50484308000
22	-3021.50484227000
23	-3021.50484172000
24	-3021.50484135000
25	-3021.50484110000
26	-3021.50484092000
27	-3021.50484081000
	???

the lowest energy is reached on the third iteration and then it steadily creeps upwards.  What gives?


From owner-chemistry@ccl.net Thu Jun 18 16:16:01 2009
From: "Aron Walsh aronjwalsh .. gmail.com" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: Force field parameters for modeling a Cr2O3 surface ?
Message-Id: <-39559-090618161502-30485-y74AjLoSK1YhPTmF+gDonA%server.ccl.net>
X-Original-From: Aron Walsh <aronjwalsh*_*gmail.com>
Content-Type: multipart/alternative; boundary=0016362836cc5331f5046ca50f19
Date: Thu, 18 Jun 2009 21:14:49 +0100
MIME-Version: 1.0


Sent to CCL by: Aron Walsh [aronjwalsh .. gmail.com]
--0016362836cc5331f5046ca50f19
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

Dear Marc,

Here is a database of potential parameters from the literature which
includes Cr and O: http://www.dfrl.ucl.ac.uk/Potentials/

Good luck!

Aron

On Thu, Jun 18, 2009 at 6:11 PM, Marc Baaden baaden]~[smplinux.de <
owner-chemistry++ccl.net> wrote:

>
> Sent to CCL by: "Marc  Baaden" [baaden%%smplinux.de]
> Dear All,
>
> A colleague of mine working on surfaces and adsorption phenomena was asking
> about (classical)
> simulations of such a surface in contact with water and potentially
> adsorbing small molecules. The
> targeted surface is Cr2O3.
>
> A quick literature search for either forcefield parameters of such a
> surface or case studies based on
> classical (eg molecular dynamics) simulations did not reveal any
> significant hits. Then again, I am
> more specialized in biological molecules, so maybe I just missed the
> relevant papers.
>
> Any pointers to papers, parameters and shared experience (on successes or
> failures) would be greatly
> appreciated,
>
> Sincerely,
> Marc Baaden
> --
> http://www.baaden.ibpc.fr/projects/mddriver/
> LBT - IBPC - CNRS - Paris>
>
>

--0016362836cc5331f5046ca50f19
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear Marc,<br><br>Here is a database of potential parameters from the liter=
ature which includes Cr and O: <a href=3D"http://www.dfrl.ucl.ac.uk/Potenti=
als/">http://www.dfrl.ucl.ac.uk/Potentials/</a><br><br>Good luck!<br><br>Ar=
on<br>
<br><div class=3D"gmail_quote">On Thu, Jun 18, 2009 at 6:11 PM, Marc Baaden=
 baaden]~[<a href=3D"http://smplinux.de">smplinux.de</a> <span dir=3D"ltr">=
&lt;<a href=3D"mailto:owner-chemistry++ccl.net">owner-chemistry++ccl.net</a>&=
gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: &quot;Marc =A0Baaden&quot; [baaden%%<a href=3D"http://smpli=
nux.de" target=3D"_blank">smplinux.de</a>]<br>
Dear All,<br>
<br>
A colleague of mine working on surfaces and adsorption phenomena was asking=
 about (classical)<br>
simulations of such a surface in contact with water and potentially adsorbi=
ng small molecules. The<br>
targeted surface is Cr2O3.<br>
<br>
A quick literature search for either forcefield parameters of such a surfac=
e or case studies based on<br>
classical (eg molecular dynamics) simulations did not reveal any significan=
t hits. Then again, I am<br>
more specialized in biological molecules, so maybe I just missed the releva=
nt papers.<br>
<br>
Any pointers to papers, parameters and shared experience (on successes or f=
ailures) would be greatly<br>
appreciated,<br>
<br>
Sincerely,<br>
Marc Baaden<br>
--<br>
<a href=3D"http://www.baaden.ibpc.fr/projects/mddriver/" target=3D"_blank">=
http://www.baaden.ibpc.fr/projects/mddriver/</a><br>
LBT - IBPC - CNRS - Paris<br>
<br>
<br>
<br>
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</blockquote></div><br>

--0016362836cc5331f5046ca50f19--