From owner-chemistry@ccl.net Fri May 16 01:01:00 2008
From: "elite 158 elite158],[gmail.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: Active site visualization software
Message-Id: <-36976-080515093148-17098-rqhiD4e5KPL0qU1fLkCUyA#,#server.ccl.net>
X-Original-From: "elite 158" <elite158,+,gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_5222_3780083.1210855005102"
Date: Thu, 15 May 2008 18:06:45 +0530
MIME-Version: 1.0


Sent to CCL by: "elite 158" [elite158(_)gmail.com]

------=_Part_5222_3780083.1210855005102
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Hello Sobia,
Check out
http://accelrys.com/

for a free visualizer ..that does more that active site visualization..:)

On 5/14/08, Elaine Meng meng---cgl.ucsf.edu <owner-chemistry#ccl.net> wrote:
>
>
> Sent to CCL by: "Elaine  Meng" [meng- -cgl.ucsf.edu]
> > On May 13, 2008, at 12:48 AM, sobia ahsan halim sobia_halim],[yahoo.comwrote:
> > Can any one kindly let me know about the free protein's active site
> characterization, building and visualizer software. Thanks.
>
>
> Hi Sobia,
> UCSF Chimera has several features that relate, and it can be downloaded
> free for noncommercial use.
>
> Related features include finding contacts, finding hydrogen bonds,
> visualizing surface properties.  If your structure is in the CASTp database,
> it will also fetch pocket volume/area information and display it in a table
> that interacts with the structure.  There is not so much building, but you
> can replace sidechains with rotamers from the Dunbrack backbone-dependent or
> Richardson rotamer libraries.
>
> We are continually adding new features, so if you do download Chimera I
> recommend getting the May 1 snapshot
> http://www.cgl.ucsf.edu/chimera/download.html#snapshots
> or an even newer daily build:
> http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
>
> The features are fully documented, and I just wrote a tutorial on binding
> site analysis that covers several of them and links to their respective
> manual pages:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng*o*cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                     http://www.cgl.ucsf.edu/home/meng/index.html>
>
>

------=_Part_5222_3780083.1210855005102
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

<div><font color="#0000ff">Hello Sobia, </font></div>
<div><font color="#0000ff">Check out </font></div>
<div><font color="#0000ff"><a href="http://accelrys.com/">http://accelrys.com/</a></font></div>
<div>&nbsp;</div>
<div>for a free visualizer ..that does more that active site visualization..:)<br>&nbsp;</div>
<div><span class="gmail_quote">On 5/14/08, <b class="gmail_sendername">Elaine Meng <a href="http://meng---cgl.ucsf.edu">meng---cgl.ucsf.edu</a></b> &lt;<a href="mailto:owner-chemistry#ccl.net">owner-chemistry#ccl.net</a>&gt; wrote:</span>
<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;Elaine&nbsp;&nbsp;Meng&quot; [meng- -<a href="http://cgl.ucsf.edu">cgl.ucsf.edu</a>]<br>&gt; On May 13, 2008, at 12:48 AM, sobia ahsan halim sobia_halim],[<a href="http://yahoo.com">yahoo.com</a> wrote:<br>
&gt; Can any one kindly let me know about the free protein&#39;s active site characterization, building and visualizer software. Thanks.<br><br><br>Hi Sobia,<br>UCSF Chimera has several features that relate, and it can be downloaded free for noncommercial use.<br>
<br>Related features include finding contacts, finding hydrogen bonds, visualizing surface properties.&nbsp;&nbsp;If your structure is in the CASTp database, it will also fetch pocket volume/area information and display it in a table that interacts with the structure.&nbsp;&nbsp;There is not so much building, but you can replace sidechains with rotamers from the Dunbrack backbone-dependent or Richardson rotamer libraries.<br>
<br>We are continually adding new features, so if you do download Chimera I recommend getting the May 1 snapshot<br><a href="http://www.cgl.ucsf.edu/chimera/download.html#snapshots">http://www.cgl.ucsf.edu/chimera/download.html#snapshots</a><br>
or an even newer daily build:<br><a href="http://www.cgl.ucsf.edu/chimera/alpha-downloads.html">http://www.cgl.ucsf.edu/chimera/alpha-downloads.html</a><br><br>The features are fully documented, and I just wrote a tutorial on binding site analysis that covers several of them and links to their respective manual pages:<br>
<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html</a><br><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html</a><br>
<br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;meng*o*<a href="http://cgl.ucsf.edu">cgl.ucsf.edu</a><br>UCSF Computer Graphics Lab and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br><br><br><br<br<br<br<br><br>E-mail to subscribers: <a href="mailto:CHEMISTRY#ccl.net">CHEMISTRY#ccl.net</a> or use:<br>
&nbsp;&nbsp;&nbsp;&nbsp; <a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br>E-mail to administrators: <a href="mailto:CHEMISTRY-REQUEST#ccl.net">CHEMISTRY-REQUEST#ccl.net</a> or use<br>
&nbsp;&nbsp;&nbsp;&nbsp; <a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br>Subscribe/Unsubscribe:<br>&nbsp;&nbsp;&nbsp;&nbsp; <a href="http://www.ccl.net/chemistry/sub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
<br>Before posting, check wait time at: <a href="http://www.ccl.net">http://www.ccl.net</a><br><br>Job: <a href="http://www.ccl.net/jobs">http://www.ccl.net/jobs</a><br>Conferences: <a href="http://server.ccl.net/chemistry/announcements/conferences/">http://server.ccl.net/chemistry/announcements/conferences/</a><br>
<br>Search Messages: <a href="http://www.ccl.net/htdig">http://www.ccl.net/htdig</a>&nbsp;&nbsp;(login: ccl, Password: search)<br><br<br>&nbsp;&nbsp;&nbsp;&nbsp; <a href="http://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.txt</a><br>
<br>RTFI: <a href="http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br><br><br></blockquote></div><br>

------=_Part_5222_3780083.1210855005102--


From owner-chemistry@ccl.net Fri May 16 01:35:00 2008
From: "David Gallagher gallagher.da _ gmail.com" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL: MOPAC2007
Message-Id: <-36977-080516005909-13188-3Nj2zZwvCfCCfgRczsR8PQ*|*server.ccl.net>
X-Original-From: "David Gallagher" <gallagher.da]*[gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_9596_6305329.1210910543136"
Date: Thu, 15 May 2008 21:02:23 -0700
MIME-Version: 1.0


Sent to CCL by: "David Gallagher" [gallagher.da^gmail.com]
------=_Part_9596_6305329.1210910543136
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

The online manual for MOPAC2007 provides some information on constructing
data sets for solids:

1. Go to http://www.openmopac.net/manual/index.html
2. Click on "Examples" (at the top of the page)
3. Then click on "How to construct a data set" (near bottom of the page)

Regards,
David Gallagher
CACheResearch.com




On Thu, May 15, 2008 at 6:08 PM, Diego G mez darkego21|-|yahoo.com <
owner-chemistry::ccl.net> wrote:

>
> Sent to CCL by: "Diego  G  mez" [darkego21:yahoo.com]
> hello!
>
> Currently, I am trying the MOPAC2007 program to do some calculations on
> solid materials.  So, I want to know if anyone know a program to create the
> imput file for a solid calculations wiht MOPAC2007.
>
> thank a lot any suggestion!!
>
> best regards...
>
>

------=_Part_9596_6305329.1210910543136
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

<div>The online manual for MOPAC2007 provides some information on constructing data sets for solids:</div>
<div>&nbsp;</div>
<div>1. Go to&nbsp;<a href="http://www.openmopac.net/manual/index.html">http://www.openmopac.net/manual/index.html</a></div>
<div>2. Click on &quot;Examples&quot; (at the top of the page)</div>
<div>3. Then click on &quot;How to construct a data set&quot; (near bottom of the page)</div>
<div>&nbsp;</div>
<div>Regards,</div>
<div>David Gallagher</div>
<div>CACheResearch.com</div>
<div>&nbsp;</div>
<div><br><br>&nbsp;</div>
<div class="gmail_quote">On Thu, May 15, 2008 at 6:08 PM, Diego G mez darkego21|-|<a href="http://yahoo.com">yahoo.com</a> &lt;<a href="mailto:owner-chemistry::ccl.net">owner-chemistry::ccl.net</a>&gt; 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;Diego &nbsp;G &nbsp;mez&quot; [darkego21:<a href="http://yahoo.com/" target="_blank">yahoo.com</a>]<br>
hello!<br><br>Currently, I am trying the MOPAC2007 program to do some calculations on solid materials. &nbsp;So, I want to know if anyone know a program to create the imput file for a solid calculations wiht MOPAC2007.<br><br>
thank a lot any suggestion!!<br><br>best regards...<br><br></blockquote></div>

------=_Part_9596_6305329.1210910543136--


From owner-chemistry@ccl.net Fri May 16 04:22:01 2008
From: "Ulrike Salzner salzner:_:fen.bilkent.edu.tr" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: ACPI-SuSE-QuadCore
Message-Id: <-36978-080516035241-7608-10fdlFQ+i4b0B7bW1+QFKQ|-|server.ccl.net>
X-Original-From: Ulrike Salzner <salzner^_^fen.bilkent.edu.tr>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-15; format=flowed
Date: Fri, 16 May 2008 10:14:30 +0300
MIME-Version: 1.0


Sent to CCL by: Ulrike Salzner [salzner-.-fen.bilkent.edu.tr]
Dear CCLers,
I bought a new QuadCore machine and installed openSuSE. The
installation did not work without switching ACPI off. Now I can get
only one processor to run. Has anyone solved this problem? Can I
configure ACPI without reinstalling and if not what should I do? A
search brought up that instead of using "ACPI=off" at boot prompt one
should write "pci=nommconf". Is this correct?
Thanks a lot,
Ulrike Salzner


From owner-chemistry@ccl.net Fri May 16 05:53:02 2008
From: "Tris Youngs t.youngs],[qub.ac.uk" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: MOPAC2007
Message-Id: <-36979-080516043335-16149-KDD471WTE2od5dBgnMkIbw]_[server.ccl.net>
X-Original-From: Tris Youngs <t.youngs##qub.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Date: Fri, 16 May 2008 08:54:21 +0100 (BST)
MIME-Version: 1.0


Sent to CCL by: Tris Youngs [t.youngs..qub.ac.uk]
Diego,

You may want to look at my own code Aten (www.projectaten.org) which 
handles the creation and editing of periodic systems, e.g. solids. An 
output filter can also be written to provide the exact input that 
MOPAC2007 requires. If you need any help with this, give me a shout.

Tris.

-- 
Dr. T. Youngs  (t.youngs#%#qub.ac.uk)
Atomistic Simulation Centre
Old Physics Building
Queens University Belfast
Belfast, BT7 1NN, N.I.

On Thu, 15 May 2008, Diego G mez darkego21|-|yahoo.com wrote:

> 
> Sent to CCL by: "Diego  G  mez" [darkego21:yahoo.com]
> hello!
> 
> Currently, I am trying the MOPAC2007 program to do some calculations on solid materials.  So, I want to know if anyone know a program to create the imput file for a solid calculations wiht MOPAC2007.
> 
> thank a lot any suggestion!!
> 
> best regards...> 
> 
>


From owner-chemistry@ccl.net Fri May 16 06:08:01 2008
From: "Sangeetha Vimal srdshigella a gmail.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: Virtual screening
Message-Id: <-36980-080516060459-3308-0+AbhS9wttQ/mlzuVX9k4Q * server.ccl.net>
X-Original-From: "Sangeetha  Vimal" <srdshigella[]gmail.com>
Date: Fri, 16 May 2008 06:04:55 -0400


Sent to CCL by: "Sangeetha  Vimal" [srdshigella[#]gmail.com]
Dear All,

Is there any tool which can help parallel processing or distributed processing of docking softwares. I am looking for a clustering tool which can make use of idle computer/processors there by enhancing faster virtual screening.

I would be glad to hear your reply.

Thanks in advance.


With regards

Sangeetha.


From owner-chemistry@ccl.net Fri May 16 07:52:01 2008
From: "Carsten Detering detering/a\biosolveit.de" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL: Virtual Screening
Message-Id: <-36981-080516065813-30324-mxi/Wp1lVFRRLrYvvOKPhw]^[server.ccl.net>
X-Original-From: "Carsten  Detering" <detering%%biosolveit.de>
Date: Fri, 16 May 2008 06:58:10 -0400


Sent to CCL by: "Carsten  Detering" [detering*biosolveit.de]

Dear Sangeetha,

If you are looking for a tool for parallel computing, try our distributor (www.biosolveit.de/distributor). It not only facilitates distributed computing on large input files, but it also serves as a pre- and post-processing tool and interfaces with most standard batch-queuing systems. 

If you have any questions, please let me know.

Cheers,
Carsten

__________________________________________________________________
Dr. Carsten Detering; Appl. Scientist      detering,biosolveit.com
Phone EU: +49-2241-2525-0 / Fax: -525           www.biosolveit.com
Phone US: +1-617-297-2770
BioSolveIT GmbH - An der Ziegelei 75 - 53757 St.Augustin - Germany
Geschftsfhrer Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261



>Is there any tool which can help parallel processing or distributed >processing of docking softwares. I am looking for a clustering tool which >can make use of idle computer/processors there by enhancing faster virtual >screening.
>
>I would be glad to hear your reply.
>
>Thanks in advance.
>
>
>With regards
>
>Sangeetha.


From owner-chemistry@ccl.net Fri May 16 11:10:00 2008
From: "David Gallagher gallagher.da]=[gmail.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: MOPAC2007 for solid state
Message-Id: <-36982-080516105658-20524-Gg8xW40bhMdebL2AiQ5nfg/./server.ccl.net>
X-Original-From: David Gallagher <gallagher.da]-[gmail.com>
Content-Type: multipart/alternative;
	boundary="=====================_4238718==.ALT"
Date: Fri, 16 May 2008 07:49:45 -0700
Mime-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da_._gmail.com]
--=====================_4238718==.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed

I forgot to mention that, if your solids are based on a repeating 
unit cell, there is a free utility called MAKPOL for constructing 
extended solids from the unit cell for input into MOPAC2007. The 
download link is at http://www.cacheresearch.com/mopac.html#mopac-support

Also, at the bottom of this page, you will find a link to a preprint 
of a new paper on using MOPAC2007 for solid state.

Regards,
David Gallagher
CACheResearch.com


At 09:02 PM 5/15/2008, David Gallagher gallagher.da _ gmail.com wrote:
>The online manual for MOPAC2007 provides some information on 
>constructing data sets for solids:
>
>1. Go to 
><http://www.openmopac.net/manual/index.html>http://www.openmopac.net/manual/index.html
>2. Click on "Examples" (at the top of the page)
>3. Then click on "How to construct a data set" (near bottom of the page)
>
>Regards,
>David Gallagher
>CACheResearch.com
>
>
>On Thu, May 15, 2008 at 6:08 PM, Diego G mez 
>darkego21|-|<http://yahoo.com>yahoo.com <<mailto:owner-chemistry * 
>ccl.net>owner-chemistry * ccl.net> wrote:
>
>Sent to CCL by: "Diego  G  mez" [darkego21:<http://yahoo.com/>yahoo.com]
>hello!
>
>Currently, I am trying the MOPAC2007 program to do some calculations 
>on solid materials.  So, I want to know if anyone know a program to 
>create the imput file for a solid calculations wiht MOPAC2007.
>thank a lot any suggestion!!
>
>best regards...

--=====================_4238718==.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<body>
I forgot to mention that, if your solids are based on a repeating unit
cell, there is a free utility called MAKPOL for constructing extended
solids from the unit cell for input into MOPAC2007. The download link is
at
<a href="http://www.cacheresearch.com/mopac.html#mopac-support" eudora="autourl">
http://www.cacheresearch.com/mopac.html#mopac-support<br><br>
</a>Also, at the bottom of this page, you will find a link to a preprint
of a new paper on using MOPAC2007 for solid state.<br><br>
Regards,<br>
David Gallagher<br>
CACheResearch.com<br><br>
<br>
At 09:02 PM 5/15/2008, David Gallagher gallagher.da _ gmail.com
wrote:<br>
<blockquote type=cite class=cite cite="">The online manual for MOPAC2007
provides some information on constructing data sets for solids:<br>
&nbsp;<br>
1. Go to
<a href="http://www.openmopac.net/manual/index.html">
http://www.openmopac.net/manual/index.html</a><br>
2. Click on &quot;Examples&quot; (at the top of the page)<br>
3. Then click on &quot;How to construct a data set&quot; (near bottom of
the page)<br>
&nbsp;<br>
Regards,<br>
David Gallagher<br>
CACheResearch.com<br>
&nbsp;<br>
<br>
On Thu, May 15, 2008 at 6:08 PM, Diego G mez
darkego21|-|<a href="http://yahoo.com">yahoo.com</a>
&lt;<a href="mailto:owner-chemistry * ccl.net">owner-chemistry *
ccl.net</a>&gt; wrote:<br>

<dl><br>

<dd>Sent to CCL by: &quot;Diego&nbsp; G&nbsp; mez&quot;
[darkego21:<a href="http://yahoo.com/">yahoo.com</a>]<br>

<dd>hello!<br><br>

<dd>Currently, I am trying the MOPAC2007 program to do some calculations
on solid materials.&nbsp; So, I want to know if anyone know a program to
create the imput file for a solid calculations wiht MOPAC2007.<br>

<dd>thank a lot any suggestion!!<br><br>

<dd>best regards...<br>

</dl></blockquote></body>
</html>

--=====================_4238718==.ALT--


From owner-chemistry@ccl.net Fri May 16 12:01:00 2008
From: "Gerard Pujadas gerard.pujadas(_)gmail.com" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL: Virtual screening
Message-Id: <-36983-080516075800-10018-PkvMr8611LRKpvyICSYVHw.:.server.ccl.net>
X-Original-From: "Gerard Pujadas" <gerard.pujadas*gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_11688_5928946.1210935811585"
Date: Fri, 16 May 2008 13:03:31 +0200
MIME-Version: 1.0


Sent to CCL by: "Gerard Pujadas" [gerard.pujadas,gmail.com]
------=_Part_11688_5928946.1210935811585
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Dear Sangeetha,


> Is there any tool which can help parallel processing or distributed
> processing of docking softwares. I am looking for a clustering tool which
> can make use of idle computer/processors there by enhancing faster virtual
> screening.
>
> I would be glad to hear your reply.
>
> Thanks in advance.
>
>
although it is not exactly what you are asking for, the eHiTS docking tool (
http://www.simbiosys.ca/ehits/) is ready for distributing docking jobs
between computers/processors. We have tested eHiTS in a single processor
computer and it gives excellent re-docking results. Moreover, eHiTS is free
for academic research.

Hope this helps

Best regards

Gerard

------=_Part_11688_5928946.1210935811585
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Dear Sangeetha,<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Is there any tool which can help parallel processing or distributed processing of docking softwares. I am looking for a clustering tool which can make use of idle computer/processors there by enhancing faster virtual screening.<br>

<br>
I would be glad to hear your reply.<br>
<br>
Thanks in advance.<br>
<br>
</blockquote><div><br>although it is not exactly what you are asking for, the eHiTS docking tool (<a href="http://www.simbiosys.ca/ehits/">http://www.simbiosys.ca/ehits/</a>) is ready for distributing docking jobs between computers/processors. We have tested eHiTS in a single processor computer and it gives excellent re-docking results. Moreover, eHiTS is free for academic research.<br>
<br>Hope this helps<br><br>Best regards<br><br>Gerard<br></div></div><br>

------=_Part_11688_5928946.1210935811585--


From owner-chemistry@ccl.net Fri May 16 12:35:01 2008
From: "Pablo A. Denis pablod/a\fq.edu.uy" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL: ACPI-SuSE-QuadCore
Message-Id: <-36984-080516073747-5490-+Ba3Dkx1C8WC5jJIHlha7w a server.ccl.net>
X-Original-From: "Pablo A. Denis" <pablod{}fq.edu.uy>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
	format=flowed;
	charset="ISO-8859-15";
	reply-type=response
Date: Fri, 16 May 2008 07:56:49 +0200
MIME-Version: 1.0


Sent to CCL by: "Pablo A. Denis" [pablod#,#fq.edu.uy]
Dear Ulrike,

                          I had the same problem last month, so I installed 
ubuntu and everything was fine. I am very happy with it.

regards,

                      pablo


----- Original Message ----- 
> From: "Ulrike Salzner salzner:_:fen.bilkent.edu.tr" 
<owner-chemistry++ccl.net>
To: "Denis, Pablo Andres " <pablod++fq.edu.uy>
Sent: Friday, May 16, 2008 9:14 AM
Subject: CCL: ACPI-SuSE-QuadCore


>
> Sent to CCL by: Ulrike Salzner [salzner-.-fen.bilkent.edu.tr]
> Dear CCLers,
> I bought a new QuadCore machine and installed openSuSE. The
> installation did not work without switching ACPI off. Now I can get
> only one processor to run. Has anyone solved this problem? Can I
> configure ACPI without reinstalling and if not what should I do? A
> search brought up that instead of using "ACPI=off" at boot prompt one
> should write "pci=nommconf". Is this correct?
> Thanks a lot,
> Ulrike Salznerhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: 
> http://server.ccl.net/chemistry/announcements/conferences/>
>
> __________ NOD32 3103 (20080516) Information __________
>
> This message was checked by NOD32 antivirus system.
> http://www.eset.com
>
>


From owner-chemistry@ccl.net Fri May 16 13:40:00 2008
From: "Simon Halstead shalstead]![hit.edu.cn" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL: Vapour reaction
Message-Id: <-36985-080516042407-11877-hh3gn/LHy+CWPgOMlQZSHw_-_server.ccl.net>
X-Original-From: Simon Halstead <shalstead_+_hit.edu.cn>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Fri, 16 May 2008 00:23:51 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Simon Halstead [shalstead|*|hit.edu.cn]

Deal CCL,

A colleague has asked me for help to perform some
simulations, but I am not sure the best way to go
about it.
He is performing some experiments on the vapourisation
of some metal and inorganic compound at opposite ends
of a tube and their subsequent reaction in the vapour
phase. He is interested in determining 

1. the ratio of the products, 
2. rates of reaction, 
3. diffusion rate 
4. temperatures at which the various products are
formed

A further complication is that both the metal and
inorganic compound are heated to different
temperatures.

I know that the diffusion can be estimated from an
NEMD simulation. I am not so clear about the others
though.

Any suggestions of methods / programs to calculate any
of these things would be most welcome.

Thanks,

Simon Halstead


From owner-chemistry@ccl.net Fri May 16 14:15:00 2008
From: "Simon Halstead shalstead a hit.edu.cn" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: Vapour reaction
Message-Id: <-36986-080516042421-12005-cPHtuNqf+Opiw+0j+Sy6nw{}server.ccl.net>
X-Original-From: Simon Halstead <shalstead[a]hit.edu.cn>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Fri, 16 May 2008 00:24:07 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Simon Halstead [shalstead]![hit.edu.cn]
Deal CCL,

A colleague has asked me for help to perform some
simulations, but I am not sure the best way to go
about it.
He is performing some experiments on the vapourisation
of some metal and inorganic compound at opposite ends
of a tube and their subsequent reaction in the vapour
phase. He is interested in determining 

1. the ratio of the products, 
2. rates of reaction, 
3. diffusion rate 
4. temperatures at which the various products are
formed

A further complication is that both the metal and
inorganic compound are heated to different
temperatures.

I know that the diffusion can be estimated from an
NEMD simulation. I am not so clear about the others
though.

Any suggestions of methods / programs to calculate any
of these things would be most welcome.

Thanks,

Simon Halstead


From owner-chemistry@ccl.net Fri May 16 15:04:01 2008
From: "Soren Eustis soreneustis^^gmail.com" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: ACPI-SuSE-QuadCore
Message-Id: <-36987-080516145505-23408-KPPi6HPLg9IjMnTD0WXSQQ : server.ccl.net>
X-Original-From: "Soren Eustis" <soreneustis!^!gmail.com>
Content-language: en-us
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
	charset="us-ascii"
Date: Fri, 16 May 2008 13:52:04 -0400
MIME-Version: 1.0


Sent to CCL by: "Soren Eustis" [soreneustis : gmail.com]
This is curious.  I installed OpenSuse 10.3 on a dual quad-core Xeon system
fairly recently with no issues regarding the multiple processors at setup.
I have checked and all 8 processors are being put to use.  

-----Original Message-----
> From: owner-chemistry!A!ccl.net [mailto:owner-chemistry!A!ccl.net] 
Sent: Friday, May 16, 2008 1:57 AM
To: Eustis, Soren 
Subject: CCL: ACPI-SuSE-QuadCore


Sent to CCL by: "Pablo A. Denis" [pablod#,#fq.edu.uy]
Dear Ulrike,

                          I had the same problem last month, so I installed 
ubuntu and everything was fine. I am very happy with it.

regards,

                      pablo


----- Original Message ----- 
> From: "Ulrike Salzner salzner:_:fen.bilkent.edu.tr" 
<owner-chemistry ~~ ccl.net>
To: "Denis, Pablo Andres " <pablod ~~ fq.edu.uy>
Sent: Friday, May 16, 2008 9:14 AM
Subject: CCL: ACPI-SuSE-QuadCore


>
> Sent to CCL by: Ulrike Salzner [salzner-.-fen.bilkent.edu.tr]
> Dear CCLers,
> I bought a new QuadCore machine and installed openSuSE. The
> installation did not work without switching ACPI off. Now I can get
> only one processor to run. Has anyone solved this problem? Can I
> configure ACPI without reinstalling and if not what should I do? A
> search brought up that instead of using "ACPI=off" at boot prompt one
> should write "pci=nommconf". Is this correct?
> Thanks a lot,
> Ulrike Salznerhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: 
> http://server.ccl.net/chemistry/announcements/conferences/>
>
> __________ NOD32 3103 (20080516) Information __________
>
> This message was checked by NOD32 antivirus system.
> http://www.eset.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Fri May 16 16:32:01 2008
From: "Karen.Green**sanofi-aventis.com" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL: Vapour reaction
Message-Id: <-36988-080516152450-8265-lh9FDXCUFRGoU9H75lzgPA|,|server.ccl.net>
X-Original-From: <Karen.Green-*-sanofi-aventis.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset="us-ascii"
Date: Fri, 16 May 2008 11:51:37 -0700
MIME-Version: 1.0


Sent to CCL by: [Karen.Green^-^sanofi-aventis.com]
Dear Simon,

I do not know your background so please forgive me if my comments are
too basic (i.e. you are already familiar with these).

It sounds like your colleague is doing experimental gas-phase molecular
beam experiments in the chemical reaction dynamics field to determine
reaction cross sections which theoretically can be used to obtain rate
constants.=20

The key reference for molecular beam experiments is:
-- Atomic and Molecular Beam Methods: Volume 1 by Giacinto Scoles et
al.(Unfortunately, this is out of print, but you might be able to find
this in your library)=20
Also, Yuan T. Lee won the Nobel Prize back in 1986(?) for this topic so
you might also search for articles by him.

I will recommend you read more on the fundamental theory of
chemical/molecular reaction dynamics.  For example, see books like:
-- Chemical Kinetics and Dynamics by Jeffrey I. Steinfeld (Author),
Joseph S. Francisco (Author), William L. Hase (Author)
-- Molecular Reaction Dynamics and Chemical Reactivity by Raphael D.
Levine (Author), R.B. Bernstein (Author)  =20
-- Reaction Dynamics (Oxford Chemistry Primers , No 61) by M. Brouard
(Author)

Hope the reaction dynamics references will help you understand the
theory and maybe others can help you with the software aspects,

Karen


-----Original Message-----
> From: owner-chemistry+*+ccl.net [mailto:owner-chemistry+*+ccl.net]=20
Sent: Friday, May 16, 2008 12:24 AM
To: Green, Karen R&D/US
Subject: CCL: Vapour reaction


Sent to CCL by: Simon Halstead [shalstead]![hit.edu.cn] Deal CCL,

A colleague has asked me for help to perform some simulations, but I am
not sure the best way to go about it.
He is performing some experiments on the vapourisation of some metal and
inorganic compound at opposite ends of a tube and their subsequent
reaction in the vapour phase. He is interested in determining=20

1. the ratio of the products,
2. rates of reaction,
3. diffusion rate
4. temperatures at which the various products are formed

A further complication is that both the metal and inorganic compound are
heated to different temperatures.

I know that the diffusion can be estimated from an NEMD simulation. I am
not so clear about the others though.

Any suggestions of methods / programs to calculate any of these things
would be most welcome.

Thanks,

Simon Halstead



-=3D This is automatically added to each message by the mailing script =
=3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20http://www.ccl.net/spammers.txt