From owner-chemistry@ccl.net Wed Dec 13 00:00:01 2006
From: "Abrash, Samuel sabrash=-=richmond.edu" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL:G: pbe functional in gaussian
Message-Id: <-33239-061212202610-20512-P68DWj9ub86Rnid2hW2K1w%x%server.ccl.net>
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Sent to CCL by: "Abrash, Samuel" [sabrash]^[richmond.edu]
You should report your choice of both exchange and correlation
functionals.  If you used pbepbe, then you're using both the pbe
exchange and correlation functionals and you should simply report that.

Sam

Samuel A. Abrash
Department of Chemistry
University of Richmond
Richmond, VA 23173
Phone:  804-289-8248
Fax:  804-287-1897
E-mail:  sabrash__richmond.edu
Web-page:  http://oncampus.richmond.edu/~sabrash
 
"Rabbi Yitzhak said:  At the time God created the world and desired to
reveal the depth of His being from out of the hidden, the light came
> from the darkness and they were joined together.  Because of this, out
of darkness came the light and out of the hidden came the revealed and
out of the good came evil and out of mercy came severe judgement, and
everything is intertwined  with everything else...the good inclination
and the evil inclination, the right and the left." - The Zohar
-----Original Message-----
> From: owner-chemistry__ccl.net [mailto:owner-chemistry__ccl.net] 
Sent: Tuesday, December 12, 2006 12:11 PM
To: Abrash, Samuel
Subject: CCL:G: pbe functional in gaussian

Sent to CCL by: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?="
[reynier.suardiaz(0)gmail.com]
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Hi
i would like to know if is correct to report that pbe functional was
used
when i put pbepbe as keyword in gaussian. My doubt is if PBE term is not
used  as some other combination of exchanges or correlation functional
where
pbe was used as one of them.
thanks in advance
reynier

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<div>Hi</div>
<div>i would like to know if is&nbsp;correct to report that pbe
functional was used when i put pbepbe as keyword in gaussian. My doubt
is if PBE term is not used&nbsp; as some other combination of exchanges
or correlation functional where pbe was used as one of them. 
</div>
<div>thanks in advance</div>
<div>reynier</div>
<div>&nbsp;</div>
<div>&nbsp;</div>

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From owner-chemistry@ccl.net Wed Dec 13 03:56:00 2006
From: "nokophala^^^aim.com" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL:G: Question about dielectric constant
Message-Id: <-33240-061213034851-6907-JtNA8j9XeB1A/V7pffb/hA ~ server.ccl.net>
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Sent to CCL by: nokophala-.-aim.com

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Hi,
Modelling pH is a tricky business. If direct interactions between the solution ions (e.g. H3O+ at low pH or OH- at high pH) and your molecule of interest take place, then  you have to explicitly include these ions to get reasonable results. On the other hand, if you are modelling long range (electrostatic) effects then pH effect will manifest itself via the electrostatic potential at the molecule site as a consequence of the surrounding ion field. I doubt if your suggested approach (changing dielectric constant) is correct even for modelling electrostatic effects, because for the same overall dielectric constant (e.g. water) the pH can vary a lot. The dielectric constant is a property of the bulk solvent, and will not change much with pH (or changes will be below range where calculations will show differences). I think explicit inclusion of some of the ions (perhaps then inserting the cluster into a continuum model of your background solvent) will be a reasonable approach.
 
Regards,
Noko Phala
Anglo Research
 
-----Original Message-----
> From: owner-chemistry-,-ccl.net
To: nokophala-,-aim.com
Sent: Wed, 13 Dec 2006 5:13 AM
Subject: CCL:G: Question about dielectric constant


Sent to CCL by: "Ana Maria Mendoza" [mwilson|*|ciad.mx]

Hi,   
I am working with the Gaussian 03W computational package. As you know, in this 
package it is not possible to simulate the pH of the medium, so I would like to 
know if it is feasible to employ HCl and/or acetic acid for simulating an acidic 
medium, water for a neutral medium, and ammonia for an alkaline medium by 
utilizing their respective dielectric constants,in order to calculate the 
molecular properties of two molecules of interest by simulating an acidic, 
neutral and alkaline medium.

Is there anybody who can help me?

Thanks in advance

Ana Mariahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________________________________________________
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<div>Hi,</div>


<div>Modelling pH is a tricky business.&nbsp;If direct interactions between&nbsp;the solution ions (e.g. H3O+ at&nbsp;low pH or OH- at high pH)&nbsp;and&nbsp;your molecule of interest take place, then &nbsp;you have to explicitly include these ions to get reasonable results. On the other hand, if you are modelling long range (electrostatic) effects then pH effect will manifest itself via the electrostatic potential at the molecule site as a consequence of the surrounding ion field.&nbsp;I doubt if your suggested approach (changing dielectric constant) is correct even for modelling electrostatic effects, because for the same overall dielectric constant (e.g. water)&nbsp;the pH can vary a lot. The dielectric constant is a property of the bulk solvent, and will not change much with pH (or changes will be below range where calculations will show differences). I think explicit inclusion of some of the ions (perhaps then inserting the cluster into a continuum model of your background solvent) will be a reasonable approach.</div>


<div>&nbsp;</div>


<div>Regards,</div>


<div>Noko Phala</div>


<div>Anglo Research</div>
&nbsp;<br>
-----Original Message-----<br>
> From: owner-chemistry-,-ccl.net<br>
To: nokophala-,-aim.com<br>
Sent: Wed, 13 Dec 2006 5:13 AM<br>
Subject: CCL:G: Question about dielectric constant<br>
<br>

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<div class=AOLPlainTextBody id=AOLMsgPart_0_76a3492c-3bdb-4cf6-9340-fe3f7ffd0399><PRE><TT>Sent to CCL by: "Ana Maria Mendoza" [mwilson|*|ciad.mx]

Hi,   
I am working with the Gaussian 03W computational package. As you know, in this 
package it is not possible to simulate the pH of the medium, so I would like to 
know if it is feasible to employ HCl and/or acetic acid for simulating an acidic 
medium, water for a neutral medium, and ammonia for an alkaline medium by 
utilizing their respective dielectric constants,in order to calculate the 
molecular properties of two molecules of interest by simulating an acidic, 
neutral and alkaline medium.

Is there anybody who can help me?

Thanks in advance

Ana MariaE-mail to subscribers: <A href="mailto:CHEMISTRY%40ccl.net">CHEMISTRY-,-ccl.net</A> or use:
      <A href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=_blank>http://www.ccl.net/cgi-bin/ccl/send_ccl_message</A>

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From owner-chemistry@ccl.net Wed Dec 13 04:30:01 2006
From: "nokophala~!~aim.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: electrostatic repulsion
Message-Id: <-33241-061213035356-7360-CvfYaKjXDQt5ufTCxTAHLA{=}server.ccl.net>
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Sent to CCL by: nokophala,,aim.com

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In GAMESS you can perform Morokuma energy decomposition analysis to partition the interaction energy between two fragments into various contributions (attarctive and repulsive terms). This is also implemented in ADF although I have no experience with it.  
 
Regards,
Noko Phala
Anglo Research 
 
-----Original Message-----
> From: owner-chemistry[-]ccl.net
To: nokophala[-]aim.com
Sent: Wed, 13 Dec 2006 6:34 AM
Subject: CCL: electrostatic repulsion


Sent to CCL by: "silviu  polosan" [Spol68\a/yahoo.com]
Hi friends,

I would like to know if someone can advice me about the calculation of 
electrostatic repulsion between two molecules (two rings actuually).

Thank you veru much.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________________________________________________
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<div>In GAMESS you can perform Morokuma energy decomposition analysis to partition the interaction energy between two fragments into various contributions (attarctive and repulsive terms).&nbsp;This is also implemented in ADF although I have no experience with it.&nbsp;&nbsp;</div>


<div>&nbsp;</div>


<div>Regards,</div>


<div>Noko Phala</div>


<div>Anglo Research&nbsp;</div>
&nbsp;<br>
-----Original Message-----<br>
> From: owner-chemistry[-]ccl.net<br>
To: nokophala[-]aim.com<br>
Sent: Wed, 13 Dec 2006 6:34 AM<br>
Subject: CCL: electrostatic repulsion<br>
<br>

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<div class=AOLPlainTextBody id=AOLMsgPart_0_09984f95-36d7-4d0a-a46f-86ecc4b9aa05><PRE><TT>Sent to CCL by: "silviu  polosan" [Spol68\a/yahoo.com]
Hi friends,

I would like to know if someone can advice me about the calculation of 
electrostatic repulsion between two molecules (two rings actuually).

Thank you veru much.E-mail to subscribers: <A href="mailto:CHEMISTRY%40ccl.net">CHEMISTRY[-]ccl.net</A> or use:
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From owner-chemistry@ccl.net Wed Dec 13 07:05:00 2006
From: "Stan van Gisbergen vangisbergen~!~scm.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: electrostatic repulsion
Message-Id: <-33242-061213070402-6301-jTKKlThOvCLwkE03HCXsVw*server.ccl.net>
X-Original-From: Stan van Gisbergen <vangisbergen[A]scm.com>
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Sent to CCL by: Stan van Gisbergen [vangisbergen{:}scm.com]

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Dear Dr. Polosan,

ADF can do a Morokuma-type energy decomposition analysis in DFT  
calculations for both open-shell and closed-shell fragments (each  
ring would be a fragment in your case).

The set up of such calculations is now very easy in the 2006 version  
of our graphical user interface, as you can quickly see from our  
online fragment tutorial:
http://www.scm.com/Doc/Doc2006.01/ADFGUI/ADFGUI_tutorial/page124.html

Further input file examples on "fragment orbitals and bond energy  
decomposition" can be found here:
http://www.scm.com/Doc/Doc2006.01/ADF/Examples/page25.html

Best regards,
Stan van Gisbergen

On Dec 13, 2006, at 10:40 AM, nokophala~!~aim.com wrote:

> Sent to CCL by: nokophala,,aim.com
>
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> Content-Transfer-Encoding: 7bit
> Content-Type: text/plain; charset="us-ascii"
>
> In GAMESS you can perform Morokuma energy decomposition analysis to  
> partition the interaction energy between two fragments into various  
> contributions (attarctive and repulsive terms). This is also  
> implemented in ADF although I have no experience with it.
>
> Regards,
> Noko Phala
> Anglo Research
>
> -----Original Message-----
>> From: owner-chemistry^^ccl.net
> To: nokophala^^aim.com
> Sent: Wed, 13 Dec 2006 6:34 AM
> Subject: CCL: electrostatic repulsion
>
>
> Sent to CCL by: "silviu  polosan" [Spol68\a/yahoo.com]
> Hi friends,
>
> I would like to know if someone can advice me about the calculation of
> electrostatic repulsion between two molecules (two rings actuually).
>
> Thank you veru much.http://www.ccl.net/cgi-bin/ccl/ 
> send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp:// 
> www.ccl.net/ 
> spammers.txt__________________________________________________________ 
> ______________
> Check Out the new free AIM(R) Mail -- 2 GB of storage and industry- 
> leading spam and email virus protection.
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> <HTML><BODY>
> <div>In GAMESS you can perform Morokuma energy decomposition  
> analysis to partition the interaction energy between two fragments  
> into various contributions (attarctive and repulsive  
> terms).&nbsp;This is also implemented in ADF although I have no  
> experience with it.&nbsp;&nbsp;</div>
>
>
> <div>&nbsp;</div>
>
>
> <div>Regards,</div>
>
>
> <div>Noko Phala</div>
>
>
> <div>Anglo Research&nbsp;</div>
> &nbsp;<br>
> -----Original Message-----<br>
>> From: owner-chemistry^^ccl.net<br>
> To: nokophala^^aim.com<br>
> Sent: Wed, 13 Dec 2006 6:34 AM<br>
> Subject: CCL: electrostatic repulsion<br>
> <br>
>
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> <div class=AOLPlainTextBody id=AOLMsgPart_0_09984f95-36d7-4d0a- 
> a46f-86ecc4b9aa05><PRE><TT>Sent to CCL by: "silviu  polosan" [Spol68 
> \a/yahoo.com]
> Hi friends,
>
> I would like to know if someone can advice me about the calculation of
> electrostatic repulsion between two molecules (two rings actuually).
>
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Dr. S.J.A. van Gisbergen
Scientific Computing & Modelling NV
Theoretical Chemistry, Vrije Universiteit
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands
vangisbergen---scm.com
http://www.scm.com
T: +31-20-5987626
F: +31-20-5987629


--Apple-Mail-55-869431711
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html;
	charset=ISO-8859-1

<HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
-khtml-line-break: after-white-space; ">Dear Dr. Polosan,<DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>ADF can do a Morokuma-type =
energy decomposition analysis in DFT calculations for both open-shell =
and closed-shell fragments (each ring would be a fragment in your =
case).</DIV><DIV><BR class=3D"khtml-block-placeholder"></DIV><DIV>The =
set up of such calculations is now very easy in the 2006 version of our =
graphical user interface, as you can quickly see from our online =
fragment tutorial:</DIV><DIV><A =
href=3D"http://www.scm.com/Doc/Doc2006.01/ADFGUI/ADFGUI_tutorial/page124.h=
tml">http://www.scm.com/Doc/Doc2006.01/ADFGUI/ADFGUI_tutorial/page124.html=
</A></DIV><DIV><BR class=3D"khtml-block-placeholder"></DIV><DIV>Further =
input file examples on "fragment orbitals and bond energy decomposition" =
can be found here:</DIV><DIV><A =
href=3D"http://www.scm.com/Doc/Doc2006.01/ADF/Examples/page25.html">http:/=
/www.scm.com/Doc/Doc2006.01/ADF/Examples/page25.html</A></DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>Best =
regards,</DIV><DIV>Stan van Gisbergen</DIV><DIV><BR><DIV><DIV>On Dec 13, =
2006, at 10:40 AM, nokophala~!~aim.com wrote:</DIV><BR =
class=3D"Apple-interchange-newline"><BLOCKQUOTE type=3D"cite"><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Sent to CCL by: nokophala,,aim.com</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">----------MB_8C8ECAB54D3E822_104C_62C5_mblk-r35.sysops.aol.com</DIV><DIV=
 style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Content-Transfer-Encoding: 7bit</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Content-Type: text/plain; =
charset=3D"us-ascii"</DIV><DIV style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; =
"><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">In GAMESS you can perform =
Morokuma energy decomposition analysis to partition the interaction =
energy between two fragments into various contributions (attarctive and =
repulsive terms). This is also implemented in ADF although I have no =
experience with it. <SPAN =
class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">Regards,</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">Noko Phala</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Anglo Research<SPAN =
class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-----Original =
Message-----</DIV> <BLOCKQUOTE type=3D"cite"><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">From: =
owner-chemistry^^ccl.net</DIV> </BLOCKQUOTE><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To: =
nokophala^^aim.com</DIV><DIV style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; ">Sent: Wed, 13 Dec 2006 6:34 =
AM</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: =
0px; margin-left: 0px; ">Subject: CCL: electrostatic repulsion</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sent to CCL =
by: "silviu<SPAN class=3D"Apple-converted-space">=A0 </SPAN>polosan" =
[Spol68\a/yahoo.com]</DIV><DIV style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; ">Hi friends,</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I would =
like to know if someone can advice me about the calculation of<SPAN =
class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">electrostatic repulsion between two molecules (two rings =
actuually).</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Thank you veru much.http://<A =
href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/=
chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt__________________=
______________________________________________________">www.ccl.net/cgi-bi=
n/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://w=
ww.ccl.net/spammers.txt___________________________________________________=
_____________________</A></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Check Out the =
new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and =
email virus protection.</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; =
">----------MB_8C8ECAB54D3E822_104C_62C5_mblk-r35.sysops.aol.com</DIV><DIV=
 style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Content-Transfer-Encoding: 7bit</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Content-Type: text/html; =
charset=3D"us-ascii"</DIV><DIV style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; =
"><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; =
">&lt;HTML&gt;&lt;BODY&gt;</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">&lt;div&gt;In =
GAMESS you can perform Morokuma energy decomposition analysis to =
partition the interaction energy between two fragments into various =
contributions (attarctive and repulsive terms).&amp;nbsp;This is also =
implemented in ADF although I have no experience with =
it.&amp;nbsp;&amp;nbsp;&lt;/div&gt;</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">&lt;div&gt;&amp;nbsp;&lt;/div&gt;</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">&lt;div&gt;Regards,&lt;/div&gt;</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">&lt;div&gt;Noko Phala&lt;/div&gt;</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">&lt;div&gt;Anglo Research&amp;nbsp;&lt;/div&gt;</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">&amp;nbsp;&lt;br&gt;</DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">-----Original Message-----&lt;br&gt;</DIV> <BLOCKQUOTE =
type=3D"cite"><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">From: =
owner-chemistry^^ccl.net&lt;br&gt;</DIV> </BLOCKQUOTE><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">To: nokophala^^aim.com&lt;br&gt;</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Sent: Wed, 13 Dec 2006 6:34 AM&lt;br&gt;</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Subject: CCL: electrostatic =
repulsion&lt;br&gt;</DIV><DIV style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; ">&lt;br&gt;</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">&lt;STYLE&gt;</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">.AOLPlainTextBody {</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><SPAN class=3D"Apple-converted-space">=A0 =A0 =
</SPAN>margin: 0px;</DIV><DIV style=3D"margin-top: 0px; margin-right: =
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From owner-chemistry@ccl.net Wed Dec 13 08:57:00 2006
From: "Yohann Moreau yohannm- -yfaat.ch.huji.ac.il" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian and forcefield
Message-Id: <-33243-061213032045-24152-fPNVwnI90/1JvIOgJRz+tg . server.ccl.net>
X-Original-From: Yohann Moreau <yohannm-,-yfaat.ch.huji.ac.il>
Content-Disposition: inline
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  charset="iso-8859-15"
Date: Wed, 13 Dec 2006 09:06:57 +0200
MIME-Version: 1.0


Sent to CCL by: Yohann Moreau [yohannm]^[yfaat.ch.huji.ac.il]
Hi Fabienne,

You can have the different terms of the forcefield and the energies associated 
by simply adding IOP(4/33=5) in your input file. 
This will make the program print the different parameters used and also the 
detail of associated energies.
As usual with iop(N/33), the size of the output file can increase 
dramatically.

Hope this helps, 

Yohann




Le mardi 12 décembre 2006 19:48, Fabienne Bessac fbessac(0)iciq.es a écrit :
> Sent to CCL by: "Fabienne  Bessac" [fbessac%%iciq.es]
> Hello everyone,
>
>   I would like to have the different terms which contribute to the MM
> energy in a Gaussian 03 calculation. I mean : Total Energy
>                         Stretch
>                            Bend
>                         Torsion
>                Improper Torsion
>                             VDW
>                   Electrostatic
>         Explicit Hydrogen Bonds
>                     Cross Terms
> Is it possible? Does anyone have modified the Gaussian code in order to
> print that?
>
>   Thanks  a lot for your help.
>
> Fabienne.

From owner-chemistry@ccl.net Wed Dec 13 09:32:00 2006
From: "Anatoli Korkin a_korkin*o*yahoo.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: News from NGC2007 in Arizona
Message-Id: <-33244-061213085703-7693-3fzysTmoW2O0YesKpHzDpQ{=}server.ccl.net>
X-Original-From: "Anatoli  Korkin" <a_korkin],[yahoo.com>
Date: Wed, 13 Dec 2006 08:57:03 -0500


Sent to CCL by: "Anatoli  Korkin" [a_korkin*_*yahoo.com]
Dear CCL members:

Technology-business interface has been added to the NGC2007 conference
program to assist developers in understanding both the opportunities and
the complexities associated with moving technology innovations from the
lab to the marketplace. To learn more about the exciting scientific and
business program of Nano & Giga Forum in Arizona and its unique networking
and social program,  read the last meeting newsletter at the conference
web site:

http://asdn.net/ngc2007/newsletters.shtml

Happy Holidays!

Anatoli Korkin
a_korkin[at]yahoo.com


From owner-chemistry@ccl.net Wed Dec 13 11:27:00 2006
From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas---chem.elte.hu" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian and forcefield
Message-Id: <-33245-061213075305-26792-kSKO6enKpedwKe585aHRQA++server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas <farkas|chem.elte.hu>
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Date: Wed, 13 Dec 2006 13:54:50 +0100
Mime-Version: 1.0


Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas]|[chem.elte.hu]
Hi Fabienne,

Use "IOp(4/33=2)" to get more detailed output from MM. Using large
number than 2 gives even more details.

Best wishes,

Ödön


On Tue, 2006-12-12 at 12:45 -0500, Fabienne Bessac fbessac(0)iciq.es
wrote:
> Sent to CCL by: "Fabienne  Bessac" [fbessac%%iciq.es]
> Hello everyone,
> 
>   I would like to have the different terms which contribute to the MM energy in a Gaussian 03 calculation. I mean :
>                    Total Energy
>                         Stretch
>                            Bend
>                         Torsion
>                Improper Torsion
>                             VDW
>                   Electrostatic
>         Explicit Hydrogen Bonds
>                     Cross Terms
> Is it possible? Does anyone have modified the Gaussian code in order to print that?
> 
>   Thanks  a lot for your help.
> 
> Fabienne.> 
> 
> 
-- 
Ödön Farkas
Research associate professor
Deparment of Organic Chemistry, 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 Wed Dec 13 12:01:01 2006
From: "Adil R Zhugralin zhugrali#bc.edu" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: NBO analysis with transition metal
Message-Id: <-33246-061213113330-26925-Z++xr5wxXGuuAN/ewEP52Q- -server.ccl.net>
X-Original-From: "Adil R Zhugralin" <zhugrali[#]bc.edu>
Date: Wed, 13 Dec 2006 11:33:30 -0500


Sent to CCL by: "Adil R Zhugralin" [zhugrali^^bc.edu]
Dear CCL'ers:

I have been trying to carry out an NBO analysis [pop=(nbo,savemixed)] on a transition metal complex (ruthenium alkylidene). Every time I tried to run this job I get the following output:
NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO) ANALYSIS:

 Highest occupied NBOs are not at the beginning of the NBO list;
 The NLMO program is not currently set up to handle this.
 Illegal range for read:  IUnit=  7 Address=      -256 Length=            -256 File length=
   32059392.
 Error termination in NtrErr:
 NtrErr called from NtrIO.

I found a post on CCL, which suggested taking offending atom and moving it to the end of the list in input (the input was in cartesian coord.) However, there are a lot of low occupancy core orbitals in the molecule. I tried to move as many of the offending atoms as possible (practically half the molecule, excluding hydrogen atoms) with ruthenium at the very bottom of the molecular specifications. The job gave exact same output as before. Any suggestions would be greatly appreciated! Thank you very much in advance.

Adil


From owner-chemistry@ccl.net Wed Dec 13 13:01:00 2006
From: "John McKelvey jmmckel|-|gmail.com" <owner-chemistry()server.ccl.net>
To: CCL
Subject: CCL: Linux for dual dual-core machines
Message-Id: <-33247-061213075320-26862-8jiVtsqljuZtRc5Gs2Jbrw()server.ccl.net>
X-Original-From: "John McKelvey" <jmmckel+*+gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_134122_24068433.1166014390381"
Date: Wed, 13 Dec 2006 07:53:10 -0500
MIME-Version: 1.0


Sent to CCL by: "John McKelvey" [jmmckel|,|gmail.com]
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Hello,

Could is ask what flavor of Linux should work best with an Asus K8N-DL with
dual dual-core AMD Opterons? [160 Gbyte NCQ Seagate SATA2 drive... more to
be added.. want to get the machine running first; 2Gbyte memory]

Thanks!

John McKelvey

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<pre>Hello,<br><br>Could is ask what flavor of Linux should work best with an Asus K8N-DL with<br>dual dual-core AMD Opterons? [160 Gbyte NCQ Seagate SATA2 drive... more to<br>be added.. want to get the machine running first; 2Gbyte memory]
<br><br>Thanks!<br><br>John McKelvey</pre>

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From owner-chemistry@ccl.net Wed Dec 13 14:51:01 2006
From: "Daniel Jana dfjana%a%gmail.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: Linux for dual dual-core machines
Message-Id: <-33248-061213144459-8759-+oVlbHnDpQb91BYMCNvVHA%a%server.ccl.net>
X-Original-From: Daniel Jana <dfjana##gmail.com>
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Date: Wed, 13 Dec 2006 20:44:47 +0100
MIME-Version: 1.0


Sent to CCL by: Daniel Jana [dfjana]^[gmail.com]
John McKelvey jmmckel|-|gmail.com wrote:
> Could is ask what flavor of Linux should work best with an Asus K8N-DL with
> dual dual-core AMD Opterons? [160 Gbyte NCQ Seagate SATA2 drive... more to
> be added.. want to get the machine running first; 2Gbyte memory]
>   

Hi,

Although I'm not an expert on the subject I'd say (and I read a bit 
about it so this is not totally out of the dark) that since dual-core 
support is at the kernel every distribution should work good with it. 
Just keep in mind that multi-cpu systems need to have the CPU 
frequencies synced, but I suppose you already knew that. So, from now on 
it's just a matter of applicability to the software you are running and 
personal preference. Have fun!

Daniel Jana


From owner-chemistry@ccl.net Wed Dec 13 15:25:00 2006
From: "Andrew D. Fant fant]^[pobox.com" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: Linux for dual dual-core machines
Message-Id: <-33249-061213151816-385-ypVT4zBISehoQe4g3/MdLQ(0)server.ccl.net>
X-Original-From: "Andrew D. Fant" <fant{:}pobox.com>
Content-Transfer-Encoding: 7bit
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Date: Wed, 13 Dec 2006 15:13:37 -0500
MIME-Version: 1.0


Sent to CCL by: "Andrew D. Fant" [fant]-[pobox.com]
John McKelvey jmmckel|-|gmail.com wrote:
> 
> Could is ask what flavor of Linux should work best with an Asus K8N-DL with
> dual dual-core AMD Opterons? [160 Gbyte NCQ Seagate SATA2 drive... more to
> be added.. want to get the machine running first; 2Gbyte memory]
> 

John,
    Any 64-bit distribution ought to work just fine with that kind of a setup.
I think the term "bog standard" describes it rather well 8-).  I'm partial to
Gentoo for my own reasons, but Debian, Fedora, and RedHat (and it's whitebox and
scientificlinux repackagings) all ought to be fine for it.  Are you going to be
using this as a workstation or as a server?

Andy

-- 
Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fant]~[pobox.com | That shines on me               | Disclaimer:  I don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myself


From owner-chemistry@ccl.net Wed Dec 13 21:04:00 2006
From: "Darryl Reid darryl.reid(~)gmail.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Linux for dual dual-core machines
Message-Id: <-33250-061213164317-18096-M4AHrSdxgMvcRhYtj2BaMw:server.ccl.net>
X-Original-From: "Darryl Reid" <darryl.reid^gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_12965_27135937.1166042546364"
Date: Wed, 13 Dec 2006 15:42:26 -0500
MIME-Version: 1.0


Sent to CCL by: "Darryl Reid" [darryl.reid(a)gmail.com]
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Hello John,

Basically any recent modern distro has specific x86_64 package, that should
work fine with it. E.g. Mandriva 2007 has 2 different packages, one for i586
(that's the 32 bit Intel/AMD version) and the other is the x86_64 which is
the one optimized for 64 bit architecture such as the AMD Opteron.

So, the "easy" way is to install such package (Fedora also has separate
package for x86_64 architecture). This will get better performance than the
32 bit version, but not the maximum possible. To get the maximum performance
out, you have to go the "hard" way and compile a kernel optimized for
Opteron, or better yet, compile every package that way, e.g. install a
source-based distribution like Gentoo fully customized for the specific
hardware. However, be warned that installing Gentoo is far more complicated
and requires some low level tinkering and configuration file editing than
installing Mandriva (which is very easy plug-n-play requires only a few
mouse
clicks).

Darryl

On 12/13/06, Andrew D. Fant fant]^[pobox.com <owner-chemistry..ccl.net>
wrote:
>
> Sent to CCL by: "Andrew D. Fant" [fant]-[pobox.com]
> John McKelvey jmmckel|-|gmail.com wrote:
> >
> > Could is ask what flavor of Linux should work best with an Asus K8N-DL
> with
> > dual dual-core AMD Opterons? [160 Gbyte NCQ Seagate SATA2 drive... more
> to
> > be added.. want to get the machine running first; 2Gbyte memory]
> >
>
> John,
>     Any 64-bit distribution ought to work just fine with that kind of a
> setup.
> I think the term "bog standard" describes it rather well 8-).  I'm partial
> to
> Gentoo for my own reasons, but Debian, Fedora, and RedHat (and it's
> whitebox and
> scientificlinux repackagings) all ought to be fine for it.  Are you going
> to be
> using this as a workstation or as a server?
>
> Andy
>
> --
> Andrew Fant    | And when the night is cloudy    | This space to let
> Molecular Geek | There is still a light          |----------------------
> fant]![pobox.com | That shines on me               | Disclaimer:  I don't
> Boston, MA     | Shine until tomorrow, Let it be | even speak for myself>
>
>
>

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Hello John, <br><br>Basically any recent modern distro has specific x86_64 package, that should<br>work fine with it. E.g. Mandriva 2007 has 2 different packages, one for i586<br>(that&#39;s the 32 bit Intel/AMD version) and the other is the x86_64 which is
<br>the one optimized for 64 bit architecture such as the AMD Opteron.<br><br>So, the &quot;easy&quot; way is to install such package (Fedora also has separate<br>package for x86_64 architecture). This will get better performance than the
<br>32 bit version, but not the maximum possible. To get the maximum performance<br>out, you have to go the &quot;hard&quot; way and compile a kernel optimized for<br>Opteron, or better yet, compile every package that way, 
e.g. install a<br>source-based distribution like Gentoo fully customized for the specific<br>hardware. However, be warned that installing Gentoo is far more complicated<br>and requires some low level tinkering and configuration file editing than
<br>installing Mandriva (which is very easy plug-n-play requires only a few mouse<br>clicks).<br><br>Darryl <br><br><div><span class="gmail_quote">On 12/13/06, <b class="gmail_sendername">Andrew D. Fant fant]^[<a href="http://pobox.com">
pobox.com</a></b> &lt;<a href="mailto:owner-chemistry..ccl.net">owner-chemistry..ccl.net</a>&gt; wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Sent to CCL by: &quot;Andrew D. Fant&quot; [fant]-[<a href="http://pobox.com">pobox.com</a>]<br>John McKelvey jmmckel|-|gmail.com wrote:<br>&gt;<br>&gt; Could is ask what flavor of Linux should work best with an Asus K8N-DL with
<br>&gt; dual dual-core AMD Opterons? [160 Gbyte NCQ Seagate SATA2 drive... more to<br>&gt; be added.. want to get the machine running first; 2Gbyte memory]<br>&gt;<br><br>John,<br>&nbsp;&nbsp;&nbsp;&nbsp;Any 64-bit distribution ought to work just fine with that kind of a setup.
<br>I think the term &quot;bog standard&quot; describes it rather well 8-).&nbsp;&nbsp;I&#39;m partial to<br>Gentoo for my own reasons, but Debian, Fedora, and RedHat (and it&#39;s whitebox and<br>scientificlinux repackagings) all ought to be fine for it.&nbsp;&nbsp;Are you going to be
<br>using this as a workstation or as a server?<br><br>Andy<br><br>--<br>Andrew Fant&nbsp;&nbsp;&nbsp;&nbsp;| And when the night is cloudy&nbsp;&nbsp;&nbsp;&nbsp;| This space to let<br>Molecular Geek | There is still a light&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;|----------------------<br>
fant]![<a href="http://pobox.com">pobox.com</a> | That shines on me&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; | Disclaimer:&nbsp;&nbsp;I don&#39;t<br>Boston, MA&nbsp;&nbsp;&nbsp;&nbsp; | Shine until tomorrow, Let it be | even speak for myself<br><br><br><br<br<br<br<br><br>E-mail to subscribers: 
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