From owner-chemistry@ccl.net Thu Nov 27 03:37:01 2008
From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas() chem.elte.hu" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL:G: Constraints?
Message-Id: <-38184-081127031146-6271-Eukia90UMSS9johhVk2CcA^-^server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas <farkas * chem.elte.hu>
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Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas]_[chem.elte.hu]
Hi David,

It is not really possible to say what to do in general in a case like
yours. Many kind of problems may occur, like the bonding of the stacked
molecules. To try to solve this choose two proper atoms (A1 and A2) in
the two molecules and add 
A1 A2 B
to get proper bonding between the stacked molecules. You might freeze
the bond angles defined for this bond then.
If zou have more choices to connect stacked molecules you might add all
of them. Of course, this will just help the description of the motions
of atoms with redundant internals and should not affect the result.

If you have further questions contact me directly.

Best wishes,

Ödön

On Mon, 2008-11-24 at 08:28 -0500, David Close closed[*]etsu.edu wrote:
> Sent to CCL by: "David  Close" [closed(~)etsu.edu]
>   I'm having a problem imposing constraints on a series of stacked molecules.  I'm trying to look at the influence of neighbors in a problem involving a crystal structure.  When I get up to three molecules in a stack the middle molecule tends to move away from the stack.  I need to impose constraints, but I keep getting a message "Curvilinear step not converged.  Error in constraints".  Thuis is in GAussian.  On another system the program seems to fuss about symmetry?
>   My questions is, what calculations are being performed to decided whether or not a constraint is suitable?  If one knows what calculations were being perfomred, is it possible to add suitable constraints? It seems as if a few bond constraints work, but when I add constrained angles, the curvilinear message appears after 100 "tries".> 
> 
-- 
Ödön Farkas
Associate professor
Deparment of Organic Chemistry and
Laboratory of Chemical Informatics,
Institute of Chemistry,
Eötvös Loránd University, Budapest
Address: 1/A Pázmány Péter sétány,
H-1117 Budapest, Hungary
Phone: +36-1-372-2570
Cell phone: +36-30-255-3111
Fax: +36-1-372-2620
URL: http://organ.elte.hu/farkas


From owner-chemistry@ccl.net Thu Nov 27 05:19:01 2008
From: "Mi Yang miyang3790*gmail.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL:G: Confusing issue of Raman intensity Vs Static polarizability
Message-Id: <-38185-081127044647-9099-gJGN5W2lUYJGB82wYne4Bg{=}server.ccl.net>
X-Original-From: "Mi  Yang" <miyang3790-$-gmail.com>
Date: Thu, 27 Nov 2008 04:46:43 -0500


Sent to CCL by: "Mi  Yang" [miyang3790~~gmail.com]
Dear Kzys!!

Yes I am a gaussian03 Rev user but Your comments a bit confusing for me as in G03 manual it is clearly mentioned that by using Freq=Raman you can "Compute Raman intensities in addition to IR intensities" so I am not understanding ur point of view.

http://www.gaussian.com/g_ur/k_freq.htm

There are some good quality of publications where they show computed raman intensities with gaussian e.g.
 J. AM. CHEM. SOC. 2005, 127, 10977-10981.pdf

http://homepage.univie.ac.at/Ferenc.Simon/publications/2005/Schaman_KBproc2005.pdf

So I have stoped my work and first want to confirm it.

Secondly, my calculated Freq value of Raman spectrum is in good agreement  to the experimental value for specific mode of vibrations after scaling. I am not comparing directlt intensity with intensity.My purpose is to show increase of intensity or activity upon intercalation of metal atom.What do you think in this regard?

I need your comments in detail especially in view of above references


> "zborowsk]|[chemia.uj.edu.pl"  wrote:
> 
> Sent to CCL by: zborowsk**chemia.uj.edu.pl
> 
> >
> > Sent to CCL by: favaro [laurent.favaro[#]u-psud.fr]
> > Do you mean that G03 does not calculate Raman Cross-section ?
> > I believe you are wrong.
> 
> Gaussian calculates Raman Activities, not Raman Intensities, and obviously
> it is not the same. Raman Activities cannot be compared directly with
> experimental Raman spectra.
> 
> Regards
> 
> Kzys
> 
> > Regards.
> > LF
> >
> > zborowsk]*[chemia.uj.edu.pl a crit :
> >> Sent to CCL by: zborowsk|,|chemia.uj.edu.pl
> >> Hi
> >> Dear Mi Yang
> >> I want to warn you if you are Gaussian user.
> >> Gaussian does not calculate  Raman Intensities
> >>
> >>
> >>
> >> Sent to CCL by: favaro [laurent.favaro|*|u-psud.fr]
> >>  Raman intensity is related to the square
> >>  of the derivative of polarizability with respect
> >>  to the normal coordinates of the vibrationnal mode.
> >>  Best regards,
> >>  Dr Favaro
> >>  Mi Yang miyang3790_+_gmail.com a crit :
> >>
> >>  Sent to CCL by: "Mi  Yang" [miyang3790*gmail.com]
> >>  Dear CCL users,
> >>  I need some comments or refs about my problem. I am studying the
> >> interaction of a metal with a boron cluster. I found the large increase
> >> of static polarizability and hyperpolarizability upon interaction of
> >> metal atom to that boron cluster. I also calculated the Raman spectrum
> >> which also showed high increase of intensity in metal boron cluster. I
> >> read some indirect relationship b/m these two properties but now in
> >> spite
> >> of my best efforts I could not find the direct relationship between
> >> Static polarizability and Raman intensity. Anybody who knows any ref or
> >> comments about this relationship (Static
> >> polarizability/hyperpolarizability and Raman intensity) would be highly
> >> appreciated.?
> >>  Miyang
> >>  P.R.China>
> >
> >
> 
> 
> -- 
> Krzysztof Zborowski
> Faculty of Chemistry
> Jagiellonian University
> 3 Ingardena Street
> 30-060 Krakow
> Poland
> phone: +48(12)632-4888 ext. 2064 or 2067
> fax:  +48(12)634-05-15
> email: zborowsk###chemia.uj.edu.pl
> gg 3817259
> skype kzys70
> www.chemia.uj.edu.pl/~zborowsk
> 
>


From owner-chemistry@ccl.net Thu Nov 27 06:47:01 2008
From: "Vasile Chis vchis[A]phys.ubbcluj.ro" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL:G: Confusing issue of Raman intensity Vs Static polarizability
Message-Id: <-38186-081127062946-5430-VYBosE0dlTprFsCw/qshpg,,server.ccl.net>
X-Original-From: "Vasile Chis" <vchis]-[phys.ubbcluj.ro>
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Date: Thu, 27 Nov 2008 13:29:30 +0200
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Sent to CCL by: "Vasile Chis" [vchis(!)phys.ubbcluj.ro]
------=_Part_28617_20562771.1227785370885
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Dear Mi Yang,


A relationship that can be used for converting calculated Raman
activities to  Raman intensities can be found, for instance, in:

P.L. Polavaru, J. Phys. Chem. 94 (1990) 8106

V. Krishnakumar, G. Keresztury, T. Sundius, R. Ramasamy, J. Mol. Struct. 702
(2004) 9.



If Freq(Raman) is specified in the route section of Gaussian, Raman
activities of normal modes and not Raman intensities are calculated. Raman
intensities depend on the exciting laser wave number and on the Boltzmann
population of the vibrational levels.



Hope this helps!



Best regards,

Vasile Chis

**=========================
Prof.dr. Vasile Chis
Babes-Bolyai University
Faculty of Physics
Kogalniceanu 1
RO-400084 Cluj-Napoca
Romania
Tel:  +40264405300
Fax: +40591906
vchis(a)phys.ubbcluj.ro
vasilechis(a)gmail.com
www.phys.ubbcluj.ro/~vchis
========================


On Thu, Nov 27, 2008 at 11:46 AM, Mi Yang miyang3790*gmail.com <
owner-chemistry(a)ccl.net> wrote:

>
> Sent to CCL by: "Mi  Yang" [miyang3790~~gmail.com]
> Dear Kzys!!
>
> Yes I am a gaussian03 Rev user but Your comments a bit confusing for me as
> in G03 manual it is clearly mentioned that by using Freq=Raman you can
> "Compute Raman intensities in addition to IR intensities" so I am not
> understanding ur point of view.
>
> http://www.gaussian.com/g_ur/k_freq.htm
>
> There are some good quality of publications where they show computed raman
> intensities with gaussian e.g.
>  J. AM. CHEM. SOC. 2005, 127, 10977-10981.pdf
>
>
> http://homepage.univie.ac.at/Ferenc.Simon/publications/2005/Schaman_KBproc2005.pdf
>
> So I have stoped my work and first want to confirm it.
>
> Secondly, my calculated Freq value of Raman spectrum is in good agreement
>  to the experimental value for specific mode of vibrations after scaling. I
> am not comparing directlt intensity with intensity.My purpose is to show
> increase of intensity or activity upon intercalation of metal atom.What do
> you think in this regard?
>
> I need your comments in detail especially in view of above references
>
>
> > "zborowsk]|[chemia.uj.edu.pl"  wrote:
> >
> > Sent to CCL by: zborowsk**chemia.uj.edu.pl
> >
> > >
> > > Sent to CCL by: favaro [laurent.favaro[#]u-psud.fr]
> > > Do you mean that G03 does not calculate Raman Cross-section ?
> > > I believe you are wrong.
> >
> > Gaussian calculates Raman Activities, not Raman Intensities, and
> obviously
> > it is not the same. Raman Activities cannot be compared directly with
> > experimental Raman spectra.
> >
> > Regards
> >
> > Kzys
> >
> > > Regards.
> > > LF
> > >
> > > zborowsk]*[chemia.uj.edu.pl a crit :
> > >> Sent to CCL by: zborowsk|,|chemia.uj.edu.pl
> > >> Hi
> > >> Dear Mi Yang
> > >> I want to warn you if you are Gaussian user.
> > >> Gaussian does not calculate  Raman Intensities
> > >>
> > >>
> > >>
> > >> Sent to CCL by: favaro [laurent.favaro|*|u-psud.fr]
> > >>  Raman intensity is related to the square
> > >>  of the derivative of polarizability with respect
> > >>  to the normal coordinates of the vibrationnal mode.
> > >>  Best regards,
> > >>  Dr Favaro
> > >>  Mi Yang miyang3790_+_gmail.com a crit :
> > >>
> > >>  Sent to CCL by: "Mi  Yang" [miyang3790*gmail.com]
> > >>  Dear CCL users,
> > >>  I need some comments or refs about my problem. I am studying the
> > >> interaction of a metal with a boron cluster. I found the large
> increase
> > >> of static polarizability and hyperpolarizability upon interaction of
> > >> metal atom to that boron cluster. I also calculated the Raman spectrum
> > >> which also showed high increase of intensity in metal boron cluster. I
> > >> read some indirect relationship b/m these two properties but now in
> > >> spite
> > >> of my best efforts I could not find the direct relationship between
> > >> Static polarizability and Raman intensity. Anybody who knows any ref
> or
> > >> comments about this relationship (Static
> > >> polarizability/hyperpolarizability and Raman intensity) would be
> highly
> > >> appreciated.?
> > >>  Miyang
> > >>  P.R.China>
> > >
> > >
> >
> >
> > --
> > Krzysztof Zborowski
> > Faculty of Chemistry
> > Jagiellonian University
> > 3 Ingardena Street
> > 30-060 Krakow
> > Poland
> > phone: +48(12)632-4888 ext. 2064 or 2067
> > fax:  +48(12)634-05-15
> > email: zborowsk###chemia.uj.edu.pl
> > gg 3817259
> > skype kzys70
> > www.chemia.uj.edu.pl/~zborowsk>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>

------=_Part_28617_20562771.1227785370885
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<div><font face="verdana,sans-serif">Dear Mi Yang,</font></div>
<div><font face="verdana,sans-serif"></font>&nbsp;</div>
<div>
<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify"><span lang="EN-US" style="COLOR: blue"><font face="verdana,sans-serif" color="#000000">A relationship that can be used for converting&nbsp;calculated Raman activities&nbsp;to&nbsp; Raman intensities can be found, for instance,&nbsp;in:</font></span></p>
<span lang="EN-US" style="COLOR: blue">
<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt 36pt; TEXT-INDENT: -36pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify; mso-layout-grid-align: none"><span lang="EN-US" style="COLOR: blue"><font color="#000000"><font face="verdana,sans-serif">P.L. Polavaru, J. Phys. Chem. 94 (1990) 8106</font></font></span></p>

<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt 36pt; TEXT-INDENT: -36pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify; mso-layout-grid-align: none"><span lang="EN-US" style="COLOR: blue"><font color="#000000"><font face="verdana,sans-serif">V. Krishnakumar, G. Keresztury, T. Sundius, R. Ramasamy, J. Mol. Struct. 702 (2004) 9.</font></font></span></p>

<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify"><font face="verdana,sans-serif" color="#000000"></font>&nbsp;</p>
<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify"><font face="verdana,sans-serif" color="#000000">If Freq(Raman) is specified in the route section of Gaussian, Raman activities of normal modes and not Raman intensities are calculated. Raman intensities depend on the exciting laser wave number and on the Boltzmann population of the vibrational levels.</font></p>

<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify"><font face="verdana,sans-serif" color="#000000"></font>&nbsp;</p>
<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify"><font face="verdana,sans-serif" color="#000000">Hope this helps!</font></p>
<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify"><font face="verdana,sans-serif" color="#000000"></font>&nbsp;</p>
<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify"><font face="verdana,sans-serif" color="#000000">Best regards,</font></p>
<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify"><font face="verdana,sans-serif" color="#000000">Vasile Chis</font></p></span>
<p class="MsoNormal" style="TEXT-JUSTIFY: inter-ideograph; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%; TEXT-ALIGN: justify"><b style="mso-bidi-font-weight: normal"><span lang="EN-US" style="COLOR: blue"></span></b>=========================<br>
Prof.dr. Vasile Chis &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br>Babes-Bolyai University &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br>Faculty of Physics &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <br>Kogalniceanu 1 &nbsp;<br>RO-400084 Cluj-Napoca<br>Romania &nbsp; &nbsp;<br>Tel: &nbsp;+40264405300 &nbsp;<br>Fax: +40591906<br>
<a href="mailto:vchis(a)phys.ubbcluj.ro">vchis(a)phys.ubbcluj.ro</a> &nbsp; &nbsp; <br><a href="mailto:vasilechis(a)gmail.com">vasilechis(a)gmail.com</a><br><a href="http://www.phys.ubbcluj.ro/~vchis">www.phys.ubbcluj.ro/~vchis</a><br>========================<br>
<br><br></p></div>
<div class="gmail_quote">On Thu, Nov 27, 2008 at 11:46 AM, Mi Yang miyang3790*<a href="http://gmail.com">gmail.com</a> <span dir="ltr">&lt;<a href="mailto:owner-chemistry(a)ccl.net">owner-chemistry(a)ccl.net</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>Sent to CCL by: &quot;Mi &nbsp;Yang&quot; [miyang3790~~<a href="http://gmail.com/" target="_blank">gmail.com</a>]<br>
Dear Kzys!!<br><br>Yes I am a gaussian03 Rev user but Your comments a bit confusing for me as in G03 manual it is clearly mentioned that by using Freq=Raman you can &quot;Compute Raman intensities in addition to IR intensities&quot; so I am not understanding ur point of view.<br>
<br><a href="http://www.gaussian.com/g_ur/k_freq.htm" target="_blank">http://www.gaussian.com/g_ur/k_freq.htm</a><br><br>There are some good quality of publications where they show computed raman intensities with gaussian e.g.<br>
&nbsp;J. AM. CHEM. SOC. 2005, 127, 10977-10981.pdf<br><br><a href="http://homepage.univie.ac.at/Ferenc.Simon/publications/2005/Schaman_KBproc2005.pdf" target="_blank">http://homepage.univie.ac.at/Ferenc.Simon/publications/2005/Schaman_KBproc2005.pdf</a><br>
<br>So I have stoped my work and first want to confirm it.<br><br>Secondly, my calculated Freq value of Raman spectrum is in good agreement &nbsp;to the experimental value for specific mode of vibrations after scaling. I am not comparing directlt intensity with intensity.My purpose is to show increase of intensity or activity upon intercalation of metal atom.What do you think in this regard?<br>
<br>I need your comments in detail especially in view of above references<br><br><br>&gt; &quot;zborowsk]|[<a href="http://chemia.uj.edu.pl/" target="_blank">chemia.uj.edu.pl</a>&quot; &nbsp;wrote:<br>&gt;<br>&gt; Sent to CCL by: zborowsk**<a href="http://chemia.uj.edu.pl/" target="_blank">chemia.uj.edu.pl</a><br>
&gt;<br>&gt; &gt;<br>&gt; &gt; Sent to CCL by: favaro [laurent.favaro[#]<a href="http://u-psud.fr/" target="_blank">u-psud.fr</a>]<br>&gt; &gt; Do you mean that G03 does not calculate Raman Cross-section ?<br>&gt; &gt; I believe you are wrong.<br>
&gt;<br>&gt; Gaussian calculates Raman Activities, not Raman Intensities, and obviously<br>&gt; it is not the same. Raman Activities cannot be compared directly with<br>&gt; experimental Raman spectra.<br>&gt;<br>&gt; Regards<br>
&gt;<br>&gt; Kzys<br>&gt;<br>&gt; &gt; Regards.<br>&gt; &gt; LF<br>&gt; &gt;<br>&gt; &gt; zborowsk]*[<a href="http://chemia.uj.edu.pl/" target="_blank">chemia.uj.edu.pl</a> a crit :<br>&gt; &gt;&gt; Sent to CCL by: zborowsk|,|<a href="http://chemia.uj.edu.pl/" target="_blank">chemia.uj.edu.pl</a><br>
&gt; &gt;&gt; Hi<br>&gt; &gt;&gt; Dear Mi Yang<br>&gt; &gt;&gt; I want to warn you if you are Gaussian user.<br>&gt; &gt;&gt; Gaussian does not calculate &nbsp;Raman Intensities<br>&gt; &gt;&gt;<br>&gt; &gt;&gt;<br>&gt; &gt;&gt;<br>
&gt; &gt;&gt; Sent to CCL by: favaro [laurent.favaro|*|<a href="http://u-psud.fr/" target="_blank">u-psud.fr</a>]<br>&gt; &gt;&gt; &nbsp;Raman intensity is related to the square<br>&gt; &gt;&gt; &nbsp;of the derivative of polarizability with respect<br>
&gt; &gt;&gt; &nbsp;to the normal coordinates of the vibrationnal mode.<br>&gt; &gt;&gt; &nbsp;Best regards,<br>&gt; &gt;&gt; &nbsp;Dr Favaro<br>&gt; &gt;&gt; &nbsp;Mi Yang miyang3790_+_<a href="http://gmail.com/" target="_blank">gmail.com</a> a crit :<br>
&gt; &gt;&gt;<br>&gt; &gt;&gt; &nbsp;Sent to CCL by: &quot;Mi &nbsp;Yang&quot; [miyang3790*<a href="http://gmail.com/" target="_blank">gmail.com</a>]<br>&gt; &gt;&gt; &nbsp;Dear CCL users,<br>&gt; &gt;&gt; &nbsp;I need some comments or refs about my problem. I am studying the<br>
&gt; &gt;&gt; interaction of a metal with a boron cluster. I found the large increase<br>&gt; &gt;&gt; of static polarizability and hyperpolarizability upon interaction of<br>&gt; &gt;&gt; metal atom to that boron cluster. I also calculated the Raman spectrum<br>
&gt; &gt;&gt; which also showed high increase of intensity in metal boron cluster. I<br>&gt; &gt;&gt; read some indirect relationship b/m these two properties but now in<br>&gt; &gt;&gt; spite<br>&gt; &gt;&gt; of my best efforts I could not find the direct relationship between<br>
&gt; &gt;&gt; Static polarizability and Raman intensity. Anybody who knows any ref or<br>&gt; &gt;&gt; comments about this relationship (Static<br>&gt; &gt;&gt; polarizability/hyperpolarizability and Raman intensity) would be highly<br>
&gt; &gt;&gt; appreciated.?<br>&gt; &gt;&gt; &nbsp;Miyang<br>&gt; &gt;&gt; &nbsp;P.R.China&gt;<br>&gt; &gt;<br>&gt; &gt;<br>&gt;<br>&gt;<br>&gt; --<br>&gt; Krzysztof Zborowski<br>&gt; Faculty of Chemistry<br>&gt; Jagiellonian University<br>
&gt; 3 Ingardena Street<br>&gt; 30-060 Krakow<br>&gt; Poland<br>&gt; phone: +48(12)632-4888 ext. 2064 or 2067<br>&gt; fax: &nbsp;+48(12)634-05-15<br>&gt; email: zborowsk###<a href="http://chemia.uj.edu.pl/" target="_blank">chemia.uj.edu.pl</a><br>
&gt; gg 3817259<br>&gt; skype kzys70<br>&gt; <a href="http://www.chemia.uj.edu.pl/~zborowsk" target="_blank">www.chemia.uj.edu.pl/~zborowsk</a><br>&gt;<br>&gt;<br><br><br><br<br<br<br<br><br>E-mail to subscribers: <a href="mailto:CHEMISTRY(a)ccl.net">CHEMISTRY(a)ccl.net</a> or use:<br>
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From owner-chemistry@ccl.net Thu Nov 27 07:22:00 2008
From: "Lukasz Cwiklik cwiklik_-_gmail.com" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: Ewald Sum
Message-Id: <-38187-081127071030-17871-Lm5wtjObSnVrqOX+nYP6fA|a|server.ccl.net>
X-Original-From: "Lukasz Cwiklik" <cwiklik() gmail.com>
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Sent to CCL by: "Lukasz Cwiklik" [cwiklik##gmail.com]
Dear Leyla,
Forces can be calculated from the potential energy. See Ch. 3 of Allen's book.
For this kind of questions see also the sources recommended by others
(Tristan and Paul) in this thread. Allen's book gives the best
explanation of Allen's source codes which you asked about but there is
much more newer/better books dealing with simulation methods.
Best and good luck,
Lukasz

-- 
Lukasz Cwiklik
http://cwiklik.wordpress.com


On Wed, Nov 26, 2008 at 2:53 AM, Leyla Ramin
l.ramin|-|aeromech.usyd.edu.au <owner-chemistry__ccl.net> wrote:
>
> Sent to CCL by: "Leyla Ramin" [l.ramin^^^aeromech.usyd.edu.au]
> Dear Lukasz,
> Thanks for your advise. However, The routine available is for
> calculation of potential energy With Ewald sum method. I am looking for
> a code for calculation the force with Ewald sum as well. Can you suggest
> something please.
> Regards
> Leila
>
>
> -----Original Message-----
>> From: owner-chemistry+lram5228==usyd.edu.au]~[ccl.net
> [mailto:owner-chemistry+lram5228==usyd.edu.au]~[ccl.net] On Behalf Of
> Lukasz Cwiklik cwiklik(!)gmail.com
> Sent: Tuesday, 25 November 2008 7:50 PM
> To: Leyla Ramin
> Subject: CCL: Ewald Sum
>
>
> Sent to CCL by: "Lukasz Cwiklik" [cwiklik%a%gmail.com]
> Dear Leyla,
> As the code is from Allen&Tildesley book look into the book for the
> details. Fortunately, the pages where the Ewald summation and the code
> are described are available for free at Google Books. Here is the link
> (Ch. 5.5.2, p. 156):
> http://tinyurl.com/626652
>
> Best,
> Lukasz
>
> --
> Lukasz Cwiklik
> http://cwiklik.wordpress.com
>
>
>
>
> On Tue, Nov 25, 2008 at 5:14 AM, Leyla Ramin lram5228%%usyd.edu.au
> <owner-chemistry * ccl.net> wrote:
>>
>> Sent to CCL by: "Leyla  Ramin" [lram5228[A]usyd.edu.au]
>> I am PhD student in Sydney university and I am working in molecular
> dynamic simulation, The codes in fortran language in your website in
> part:sources, allen-tildesley-book
> "http://www.ccl.net/cca/software/SOURCES/FORTRAN/allen-tildesley-book/in
> dex.shtml>"
>> is so useful for me.
>> In the "FICHE F.22.  ROUTINES TO PERFORM THE EWALD SUM" the routine is
>> so complicated to understand the method. I am wondering if I can get
> more information about this code.
>> Please kindly advise me and thanks for your consideration.
>>
>> Best Regards
>> Leyla Ramin>
>>
>>
>
>
>
> --
> Lukasz Cwiklik
> http://cwiklik.wordpress.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt
>
>
> - This is automatically added to each message by the mailing script ->
>
>


From owner-chemistry@ccl.net Thu Nov 27 07:56:00 2008
From: "willsd ~ appstate.edu" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL:G: Confusing issue of Raman intensity Vs Static polarizability
Message-Id: <-38188-081127073155-32286-54DO3jncuE1sLWiNpsv0mg##server.ccl.net>
X-Original-From: <willsd__appstate.edu>
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Date: Thu, 27 Nov 2008 12:31:33 GMT
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Sent to CCL by: [willsd_+_appstate.edu]
If the problem here is an attempt to compare theoretical calculations with
measured Raman spectra, there are (in addition to the things described here) two
more issues.
1: The measured Raman (conventional, NOT resonance Raman nor SERS) spectrum will
depend on the type of light detection in the spectrometer.  The equations that
connect measured intensity with computed activity are different for photon
counting versus power detection.
2: The experimental spectrum also depends quite strongly on the wavelength
dependent response of the spectrometer.  This can only be accounted for by
careful calibration of the entire spectrometer.  This requires measuring the
spectrum of a light source whose emission spectrum is known; this is usually a
blackbody source at a known temperature.
There is a recent paper by Williams, Johnson, Kitchens, and Gibbons (in TCA)
that describes these issues and reviews some of the literature on the subject. 
The paper also makes some specific recommendations about using Raman activities,
computed by Gaussian, from different theoretical models, HF, several DFT
methods, and MP2.  The main conclusion was that basis set is probably more
important than level of theory, and that CH (and very likely other XH)
stretching vibrations are likely to be poorly computed due to their strongly
anharmonic nature.
Steve Williams

----- Original Message -----
> From: "Vasile Chis vchis[A]phys.ubbcluj.ro" <owner-chemistry*o*ccl.net>
Date: Thursday, November 27, 2008 6:57 am
Subject: CCL:G: Confusing issue of Raman intensity Vs Static polarizability
To: "Williams, Steve " <willsd*o*conrad.appstate.edu>

> Dear Mi Yang,
> 
> 
> A relationship that can be used for converting calculated Raman
> activities to  Raman intensities can be found, for instance, in:
> 
> P.L. Polavaru, J. Phys. Chem. 94 (1990) 8106
> 
> V. Krishnakumar, G. Keresztury, T. Sundius, R. Ramasamy, J. Mol. 
> Struct. 702
> (2004) 9.
> 
> 
> 
> If Freq(Raman) is specified in the route section of Gaussian, Raman
> activities of normal modes and not Raman intensities are 
> calculated. Raman
> intensities depend on the exciting laser wave number and on the 
> Boltzmannpopulation of the vibrational levels.
> 
> 
> 
> Hope this helps!
> 
> 
> 
> Best regards,
> 
> Vasile Chis
> 
> **=========================
> Prof.dr. Vasile Chis
> Babes-Bolyai University
> Faculty of Physics
> Kogalniceanu 1
> RO-400084 Cluj-Napoca
> Romania
> Tel:  +40264405300
> Fax: +40591906
> vchis-x-phys.ubbcluj.ro
> vasilechis-x-gmail.com
> www.phys.ubbcluj.ro/~vchis
> ========================
> 
> 
> On Thu, Nov 27, 2008 at 11:46 AM, Mi Yang miyang3790*gmail.com <
> owner-chemistry-x-ccl.net> wrote:
> 
> >
> > Sent to CCL by: "Mi  Yang" [miyang3790~~gmail.com]
> > Dear Kzys!!
> >
> > Yes I am a gaussian03 Rev user but Your comments a bit confusing 
> for me as
> > in G03 manual it is clearly mentioned that by using Freq=Raman 
> you can
> > "Compute Raman intensities in addition to IR intensities" so I am 
> not> understanding ur point of view.
> >
> > http://www.gaussian.com/g_ur/k_freq.htm
> >
> > There are some good quality of publications where they show 
> computed raman
> > intensities with gaussian e.g.
> >  J. AM. CHEM. SOC. 2005, 127, 10977-10981.pdf
> >
> >
> > 
>
http://homepage.univie.ac.at/Ferenc.Simon/publications/2005/Schaman_KBproc2005.pdf>
> > So I have stoped my work and first want to confirm it.
> >
> > Secondly, my calculated Freq value of Raman spectrum is in good 
> agreement>  to the experimental value for specific mode of 
> vibrations after scaling. I
> > am not comparing directlt intensity with intensity.My purpose is 
> to show
> > increase of intensity or activity upon intercalation of metal 
> atom.What do
> > you think in this regard?
> >
> > I need your comments in detail especially in view of above 
> references>
> >
> > > "zborowsk]|[chemia.uj.edu.pl"  wrote:
> > >
> > > Sent to CCL by: zborowsk**chemia.uj.edu.pl
> > >
> > > >
> > > > Sent to CCL by: favaro [laurent.favaro[#]u-psud.fr]
> > > > Do you mean that G03 does not calculate Raman Cross-section ?
> > > > I believe you are wrong.
> > >
> > > Gaussian calculates Raman Activities, not Raman Intensities, and
> > obviously
> > > it is not the same. Raman Activities cannot be compared 
> directly with
> > > experimental Raman spectra.
> > >
> > > Regards
> > >
> > > Kzys
> > >
> > > > Regards.
> > > > LF
> > > >
> > > > zborowsk]*[chemia.uj.edu.pl a crit :
> > > >> Sent to CCL by: zborowsk|,|chemia.uj.edu.pl
> > > >> Hi
> > > >> Dear Mi Yang
> > > >> I want to warn you if you are Gaussian user.
> > > >> Gaussian does not calculate  Raman Intensities
> > > >>
> > > >>
> > > >>
> > > >> Sent to CCL by: favaro [laurent.favaro|*|u-psud.fr]
> > > >>  Raman intensity is related to the square
> > > >>  of the derivative of polarizability with respect
> > > >>  to the normal coordinates of the vibrationnal mode.
> > > >>  Best regards,
> > > >>  Dr Favaro
> > > >>  Mi Yang miyang3790_+_gmail.com a crit :
> > > >>
> > > >>  Sent to CCL by: "Mi  Yang" [miyang3790*gmail.com]
> > > >>  Dear CCL users,
> > > >>  I need some comments or refs about my problem. I am 
> studying the
> > > >> interaction of a metal with a boron cluster. I found the large
> > increase
> > > >> of static polarizability and hyperpolarizability upon 
> interaction of
> > > >> metal atom to that boron cluster. I also calculated the 
> Raman spectrum
> > > >> which also showed high increase of intensity in metal boron 
> cluster. I
> > > >> read some indirect relationship b/m these two properties but 
> now in
> > > >> spite
> > > >> of my best efforts I could not find the direct relationship 
> between> > >> Static polarizability and Raman intensity. Anybody 
> who knows any ref
> > or
> > > >> comments about this relationship (Static
> > > >> polarizability/hyperpolarizability and Raman intensity) 
> would be
> > highly
> > > >> appreciated.?
> > > >>  Miyang
> > > >>  P.R.China>
> > > >
> > > >
> > >
> > >
> > > --
> > > Krzysztof Zborowski
> > > Faculty of Chemistry
> > > Jagiellonian University
> > > 3 Ingardena Street
> > > 30-060 Krakow
> > > Poland
> > > phone: +48(12)632-4888 ext. 2064 or 2067
> > > fax:  +48(12)634-05-15
> > > email: zborowsk###chemia.uj.edu.pl
> > > gg 3817259
> > > skype kzys70
> > > www.chemia.uj.edu.pl/~zborowsk>
> >
> >
> > --
> > This message has been scanned for viruses and
> > dangerous content by MailScanner, and is
> > believed to be clean.
> >
> >
>


From owner-chemistry@ccl.net Thu Nov 27 08:31:01 2008
From: "favaro laurent.favaro]=[u-psud.fr" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL:G: Raman intensity Vs Static polarizability
Message-Id: <-38189-081126192047-17968-vOX1nT11TlmNa19kctST8A . server.ccl.net>
X-Original-From: favaro <laurent.favaro++u-psud.fr>
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Date: Thu, 27 Nov 2008 00:29:16 +0100
MIME-Version: 1.0


Sent to CCL by: favaro [laurent.favaro _ u-psud.fr]
For sure.
Units are expressive : (Angstroms)exp(4)/ Atomic Mass Unit
should not be compared with experimental intensity units.
Despite, trends, for similar compounds, are very interesting.
Even experiments are very difficult to compare.
Absolute intensity measures are challenging.
Best regards
L.F.

zborowsk]|[chemia.uj.edu.pl a écrit :
> Sent to CCL by: zborowsk**chemia.uj.edu.pl
>
>   
>> Sent to CCL by: favaro [laurent.favaro[#]u-psud.fr]
>> Do you mean that G03 does not calculate Raman Cross-section ?
>> I believe you are wrong.
>>     
>
> Gaussian calculates Raman Activities, not Raman Intensities, and obviously
> it is not the same. Raman Activities cannot be compared directly with
> experimental Raman spectra.
>
> Regards
>
> Kzys
>
>   
>> Regards.
>> LF
>>
>> zborowsk]*[chemia.uj.edu.pl a écrit :
>>     
>>> Sent to CCL by: zborowsk|,|chemia.uj.edu.pl
>>> Hi
>>> Dear Mi Yang
>>> I want to warn you if you are Gaussian user.
>>> Gaussian does not calculate  Raman Intensities
>>>
>>>
>>>
>>> Sent to CCL by: favaro [laurent.favaro|*|u-psud.fr]
>>>  Raman intensity is related to the square
>>>  of the derivative of polarizability with respect
>>>  to the normal coordinates of the vibrationnal mode.
>>>  Best regards,
>>>  Dr Favaro
>>>  Mi Yang miyang3790_+_gmail.com a écrit :
>>>
>>>  Sent to CCL by: "Mi  Yang" [miyang3790*gmail.com]
>>>  Dear CCL users,
>>>  I need some comments or refs about my problem. I am studying the
>>> interaction of a metal with a boron cluster. I found the large increase
>>> of static polarizability and hyperpolarizability upon interaction of
>>> metal atom to that boron cluster. I also calculated the Raman spectrum
>>> which also showed high increase of intensity in metal boron cluster. I
>>> read some indirect relationship b/m these two properties but now in
>>> spite
>>> of my best efforts I could not find the direct relationship between
>>> Static polarizability and Raman intensity. Anybody who knows any ref or
>>> comments about this relationship (Static
>>> polarizability/hyperpolarizability and Raman intensity) would be highly
>>> appreciated.?
>>>  Miyang
>>>  P.R.China>
>>>       
>>     
>
>
>


From owner-chemistry@ccl.net Thu Nov 27 09:07:01 2008
From: "Sobia Ahsan halim sobia_halim!A!yahoo.com" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: How to define water molecules during docking?????????
Message-Id: <-38190-081127085229-30713-ddcALX4uuNlaS4UWy3N0Yg|a|server.ccl.net>
X-Original-From: "Sobia Ahsan halim" <sobia_halim+/-yahoo.com>
Date: Thu, 27 Nov 2008 08:52:25 -0500


Sent to CCL by: "Sobia Ahsan halim" [sobia_halim[#]yahoo.com]
Dear All
Hi
I need to ask how to define water molecules during docking with the Autodocktools and MOE. As I found no option to define water during docking with  both of these programs. If any one know about it kindly let me know. Thanks in advance.

Regards,
Sobia.


From owner-chemistry@ccl.net Thu Nov 27 09:41:00 2008
From: "zborowsk=chemia.uj.edu.pl" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL:G: Confusing issue of Raman intensity Vs Static polarizability
Message-Id: <-38191-081127091345-14229-qijkChqsSs1VzCRETZ2PMw * server.ccl.net>
X-Original-From: zborowsk#chemia.uj.edu.pl
Content-Transfer-Encoding: 8bit
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Date: Thu, 27 Nov 2008 15:13:33 +0100 (CET)
MIME-Version: 1.0


Sent to CCL by: zborowsk---chemia.uj.edu.pl
> Sent to CCL by: "Mi  Yang" [miyang3790~~gmail.com]
> Dear Kzys!!
>
> Yes I am a gaussian03 Rev user but Your comments a bit confusing for me as
> in G03 manual it is clearly mentioned that by using Freq=Raman you can
> "Compute Raman intensities in addition to IR intensities" so I am not
> understanding ur point of view.

Yes, it is true. It is true that in the Gaussian manual is clearly
mentioned that the program calculates Raman Intensities. But this
statement is not true, Gaussian does not serve Raman Intensities directly.
This is the reason of many mistakes. I do not know why Gaussian team does
not correct its manual.

I think that Vasile Chis clear some things in His letter. I can only add
that relationship that can be used for converting calculated Raman
activities to  Raman intensities can be found also in

Michalska, Wysokinski, Chemical Physics Letters 403 (2005) 211–217

I think that the authors of this publication can send anyone free software
for calculation of Raman Intensities from Gaussian output

>
> http://www.gaussian.com/g_ur/k_freq.htm
>
> There are some good quality of publications where they show computed raman
> intensities with gaussian e.g.
>  J. AM. CHEM. SOC. 2005, 127, 10977-10981.pdf
>
> http://homepage.univie.ac.at/Ferenc.Simon/publications/2005/Schaman_KBproc2005.pdf
>
> So I have stoped my work and first want to confirm it.
>
> Secondly, my calculated Freq value of Raman spectrum is in good agreement
> to the experimental value for specific mode of vibrations after scaling. I
> am not comparing directlt intensity with intensity.My purpose is to show
> increase of intensity or activity upon intercalation of metal atom.What do
> you think in this regard?
>
> I need your comments in detail especially in view of above references

In this case maybe you do not have to transform Raman Activities from
Gaussian into Raman Intensities. Of course bigger Raman Activity denote
stronger Raman Intensity for a particular band. The problem occur if you
want to reproduce the shape of whole raman spectrum for a molecule. On the
other hand calculation of Raman Intensities from Raman Activities is not
very complicated.

Regards

Kzys


From owner-chemistry@ccl.net Thu Nov 27 11:34:00 2008
From: "Jean-Christophe Poully poully.,,.galilee.univ-paris13.fr" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: Conformational searches with right Ramachandran angles
Message-Id: <-38192-081127111033-28476-0ty7gEKGZISni6/EAg+nZw,,server.ccl.net>
X-Original-From: Jean-Christophe Poully <poully|galilee.univ-paris13.fr>
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Date: Thu, 27 Nov 2008 17:10:26 +0100
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Sent to CCL by: Jean-Christophe Poully [poully()galilee.univ-paris13.fr]
--=====================_198473968==.ALT
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Dear all,

I would like to know if there is one software=20
that can perform accurate conformational searches=20
on peptides containing at least 5 amino acids and=20
that have the ability to speed up the calculation=20
by scanning only Ramachandran angles compatible=20
with typical structures like alpha-helix and=20
beta-sheet... Most of the conformational search=20
softwares do a Monte-Carlo or systematic search,=20
but the majority of the structures found have not=20
allowed Ramachandran angles. Thank you very much by advance!




Jean-Christophe Poully

Doctorant dans l'=E9quipe AMIBES
Laboratoire de Physique des Lasers
Institut Galil=E9e
99, avenue JB Cl=E9ment
93430 VILLETANEUSE

Bureau B002
0149403853=20
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Content-Type: text/html; charset="iso-8859-1"
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<html>
<body>
<br>
Dear all,<br><br>
I would like to know if there is one software that can perform accurate
conformational searches on peptides containing at least 5 amino acids and
that have the ability to speed up the calculation by scanning <i>only</i>
Ramachandran angles compatible with typical structures like alpha-helix
and beta-sheet... Most of the conformational search softwares do a
Monte-Carlo or systematic search, but the majority of the structures
found have not allowed Ramachandran angles. Thank you very much by
advance!<br><br>
<br><br>
<x-sigsep><p></x-sigsep>
Jean-Christophe Poully<br><br>
Doctorant dans l'=E9quipe AMIBES<br>
Laboratoire de Physique des Lasers<br>
Institut Galil=E9e<br>
99, avenue JB Cl=E9ment<br>
93430 VILLETANEUSE<br><br>
Bureau B002<br>
0149403853</body>
</html>

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