From owner-chemistry@ccl.net Tue Dec  8 01:25:00 2009
From: "MUhammad Ramzan Saeed Ashraf Janjua dr_janjua2010.:.yahoo.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: How can we use OEP and LC-BLYP in ADF in-put file?
Message-Id: <-40876-091208012252-15831-7sPiFVvmRd63Dc49rb2IFw .. server.ccl.net>
X-Original-From: "MUhammad Ramzan Saeed Ashraf   Janjua" <dr_janjua2010:+:yahoo.com>
Date: Tue, 8 Dec 2009 01:22:48 -0500


Sent to CCL by: "MUhammad Ramzan Saeed Ashraf   Janjua" [dr_janjua2010:-:yahoo.com]
Dear Colleagues:
Can we use OEP and LC-BLYp functionals in ADF? If yes then How can we write their key words in in-put file of ADF.

I use Density Functional as under:

XC
LDA ALDA
GGA LB94
End

Please! let me know about OEP and LC-BLYP?

Thanks in advance!

Janjua, Muhammad Ramzan Saeed Ashraf
PhD (Physical Chemistry)
Electronic mail: janjua%%nenu.edu.cn
Peoples Republic of China


From owner-chemistry@ccl.net Tue Dec  8 10:49:01 2009
From: "Muhammad Ramzan Saeed Ashraf Janjua janjua#,#nenu.edu.cn" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: How can we use OEP and LC-BLYP in ADF in-put file?
Message-Id: <-40877-091208011745-15309-baChLHvtvLK/L7BS2f6aEw(-)server.ccl.net>
X-Original-From: "Muhammad Ramzan Saeed Ashraf  Janjua" <janjua*|*nenu.edu.cn>
Date: Tue, 8 Dec 2009 01:17:40 -0500


Sent to CCL by: "Muhammad Ramzan Saeed Ashraf  Janjua" [janjua- -nenu.edu.cn]
Dear Colleagues:
Can we use OEP and LC-BLYp functionals in ADF? If yes then How can we write their key words in in-put file of ADF.

I use Density Functional as under:

XC
LDA ALDA
GGA LB94
End

Please! let me know about OEP and LC-BLYP?

Thanks in advance!

Janjua, Muhammad Ramzan Saeed Ashraf
PhD (Physical Chemistry)
Electronic mail: dr_janjua2010-x-yahoo.com
Peoples Republic of China


From owner-chemistry@ccl.net Tue Dec  8 11:24:00 2009
From: "mi yang agri_chemist(~)yahoo.com" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: Removing Negative Frequency without reducing symmetry co
Message-Id: <-40878-091208042516-5818-0D3mwmnFJdmfLiQv9SJ1uw:+:server.ccl.net>
X-Original-From: "mi  yang" <agri_chemist^yahoo.com>
Date: Tue, 8 Dec 2009 04:25:12 -0500


Sent to CCL by: "mi  yang" [agri_chemist|-|yahoo.com]
Dear CCL users,
I have optimized a complex containing hydroborane cage with a metal atom constraining it to C2v symmetry. Now I got a negative frequency of about 123Cm-1. 

Can I finish the negative frequency without reducing the symmetry because other complexes are also in the same C2v constrains?

Miyang

agri_chemist##yahoo.com


From owner-chemistry@ccl.net Tue Dec  8 12:37:01 2009
From: "Elaine C Meng meng!^!cgl.ucsf.edu" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: new Chimera release
Message-Id: <-40879-091208120819-11639-MJHR9TE2ze2CdY2EbeVBug-#-server.ccl.net>
X-Original-From: "Elaine C Meng" <meng[-]cgl.ucsf.edu>
Date: Tue, 8 Dec 2009 12:08:15 -0500


Sent to CCL by: "Elaine C Meng" [meng-*-cgl.ucsf.edu]
Hi everybody,
A new production release of UCSF Chimera (version 1.4)
is now available from:
http://www.cgl.ucsf.edu/chimera/download.html

Download is free for noncommercial use.  Chimera is
available for Windows, Mac Aqua, Mac/X11, and Linux. 
The download includes full documentation and tutorials.

Many improvements and new features have been added since the 
previous production release (Dec 2008), as listed in the
release notes:
http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.4.html

For the time-challenged, here are just a few of the reasons 
you may want to use the new version:

1) appearance: 
 - friendlier initial display, similar to ribbons preset
 - CA-only and P-only structures can be shown as smooth tubes
 - rings can be filled, aromatic rings shown with circles
 - improved transparent surfaces (single-layer, etc.)
 - glossy lighting option on many platforms
 - anisotropic B-factors can be shown as ellipsoids
 - surface coloring by Coulombic electrostatic potential
 - 2D labels new font options, can be hidden/shown
 - labels can be moved with the mouse
 - improved single-sequence display
 - offscreen rendering on most platforms
2) I/O:
 - Blast protein tool uses Web service hosted by our lab;
   * hits can be shown as sequence alignment
   * corresponding structures (if any) can be retrieved
 - new fetch type EMDB with keyword search
 - can set download directory for caching fetched files
 - Gromacs 4 trajectories supported
3) analysis and editing:
 - planes can be defined from sets of atoms, used in 
   distance and angle measurements (with atoms and axes)
 - many more options for volume data filtering, processing  
 - new measure command performs several calculations
   on structures, surfaces, and maps
 - structure-based sequence alignment tool (Match->Align)
   can iterate to consistency
4) scripting:
 - improved  movement commands (rock, roll, turn, move,
   reset), visual effect commands (surftransparency, set),
   new commands (coordset, fly, pause) for movie scripting
 - volume planes playback (volume command)
 - bond rotation (rotation command)
 - nucleotide displays (nucleotides)
 - symmetry copy generation (sym)
 - runscript command for running python scripts
   with command-line arguments

See the release notes and User's Guide for more details. 

Enjoy!
On behalf of the Chimera team,
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


From owner-chemistry@ccl.net Tue Dec  8 13:19:01 2009
From: "Serdar Badoglu sbadoglu]![gazi.edu.tr" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL:G: Server system for Gaussian
Message-Id: <-40880-091208131735-9764-Ii1/JNW9XCKJtAQwiGP20A .. server.ccl.net>
X-Original-From: "Serdar  Badoglu" <sbadoglu(_)gazi.edu.tr>
Date: Tue, 8 Dec 2009 13:17:31 -0500


Sent to CCL by: "Serdar  Badoglu" [sbadoglu()gazi.edu.tr]
Dear CCLers, 

We are intended to buy a server system to do our Gaussian calculations, and we are planning to expand our hardware in the future. As a start, we have collected several proposals from companies. First of all, I wonder if the below cheap systems are good or not for computational uses:

1- HP DL160G6 with two quad core CPUs, 4GB memory and 160GB HDD
2- HP DL380G6 with two quad core CPUs, 4GB memory and 2 x 146GB HDD
3- Fujitsu-Siemens system (content is not clear yet)

Besides I'd like to know what kind of servers you use in your calculations. As experienced users, what would you suggest us?

Regards.


From owner-chemistry@ccl.net Tue Dec  8 15:43:01 2009
From: "Joe Corkery jcorkery#%#eyesopen.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: OpenEye CUP 11 meeting open for registration
Message-Id: <-40881-091208132244-13184-aK4FZLVdz8QrFu5qltcq7A .. server.ccl.net>
X-Original-From: Joe Corkery <jcorkery{=}eyesopen.com>
Content-Language: en-US
Content-Type: multipart/alternative;
	boundary="_000_BB3CCF2D3D6B094D96588383620C5F3E4C7029DACFEXVMBX01811ex_"
Date: Tue, 8 Dec 2009 10:22:21 -0800
MIME-Version: 1.0


Sent to CCL by: Joe Corkery [jcorkery{=}eyesopen.com]
--_000_BB3CCF2D3D6B094D96588383620C5F3E4C7029DACFEXVMBX01811ex_
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

Dear Colleague,



OpenEye's 11th annual CUP meeting will be held from Monday, March 8th to We=
dnesday, March 10th, 2010 in Santa Fe, New Mexico at the Eldorado Hotel. Th=
e six sessions we intend to cover are:



Monday morning: "Practical Electrostatics - how far do we have to go?"

--Evaluations of what the current state-of-the-art can and can't calculate.



Monday afternoon: "Statistical reasoning in molecular modeling"

--How best to use the information we have, whether from ligands, proteins o=
r literature.



Tuesday morning: "Careful, that thing is loaded - optimizing the interactio=
n between Medicinal Chemistry and Modeling" (Pat Walters, guest organizer) =
--It doesn't matter how good your work is if the chemists ignore it.



Tuesday afternoon: "MMPB: Panacea, useful or useless?"

--Some rely on it, some find it useful and some can't get anything out of i=
t at all. Some leading lights will be asked to give their opinion.



Wednesday morning: "Fragment-based Drug Discovery: Primary tool or tactic o=
f last resort?"

--What and when is the appropriate use of FBDD?



Wednesday afternoon: "New technology and old dogs"

--Workflows, GPUs and clouds, oh my! Plus a round-table: "Graphical scripti=
ng: Programming beyond our competence?"



There is still room in some sessions for contributed talks - contact me if =
you are interested. Last year our Monday night poster session was tremendou=
s, so please think about contributing this way even if you don't think you =
can manage a talk. This year our Levinthal speaker will be Dr. Ajay Jain fr=
om UCSF, who will present his talk: "Molecular Evolution: The Created and t=
he Creators and the Puzzle of Design", after the Tuesday afternoon session.=
  And for the practically inclined, we are bookending CUP with two technica=
l sessions; one at 2pm on Sunday afternoon led by Bob Tolbert on OE toolkit=
s, and one starting at 9am on Thursday morning led by Joe Corkery on adapti=
ng VIDA to enterprise-wide tasks.



As always, there is no registration cost for CUP and we feed you Monday nig=
ht at the posters and at the conference dinner Wednesday night. To register=
 for CUP 11, please go to:



http://www.eyesopen.com/forms/cup11_reg.html



If you wish to stay at the conference hotel, please contact the Eldorado Ho=
tel, (www.eldoradohotel.com<http://www.eldoradohotel.com>, 505-988-4455). W=
e have a block of rooms reserved so ask for the OpenEye rate ($159) when ma=
king your reservation by phone or enter the special promotions code '247' i=
f you use their website. Finally, in the last year American Airlines has st=
arted operating daily flights between Santa Fe and Los Angeles and Dallas/F=
ort Worth. Santa Fe airport is about a 15 minute taxi ride from downtown.



Look forward to seeing you there,



Anthony


--_000_BB3CCF2D3D6B094D96588383620C5F3E4C7029DACFEXVMBX01811ex_
Content-Type: text/html; charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:v=3D"urn:schemas-microsoft-com:vml" xmlns:o=3D"urn:schemas-micr=
osoft-com:office:office" xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns:x=3D"urn:schemas-microsoft-com:office:excel" xmlns:p=3D"urn:schemas-m=
icrosoft-com:office:powerpoint" xmlns:a=3D"urn:schemas-microsoft-com:office=
:access" xmlns:dt=3D"uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns:s=3D"=
uuid:BDC6E3F0-6DA3-11d1-A2A3-00AA00C14882" xmlns:rs=3D"urn:schemas-microsof=
t-com:rowset" xmlns:z=3D"#RowsetSchema" xmlns:b=3D"urn:schemas-microsoft-co=
m:office:publisher" xmlns:ss=3D"urn:schemas-microsoft-com:office:spreadshee=
t" xmlns:c=3D"urn:schemas-microsoft-com:office:component:spreadsheet" xmlns=
:odc=3D"urn:schemas-microsoft-com:office:odc" xmlns:oa=3D"urn:schemas-micro=
soft-com:office:activation" xmlns:html=3D"http://www.w3.org/TR/REC-html40" =
xmlns:q=3D"http://schemas.xmlsoap.org/soap/envelope/" xmlns:rtc=3D"http://m=
icrosoft.com/officenet/conferencing" xmlns:D=3D"DAV:" xmlns:Repl=3D"http://=
schemas.microsoft.com/repl/" xmlns:mt=3D"http://schemas.microsoft.com/share=
point/soap/meetings/" xmlns:x2=3D"http://schemas.microsoft.com/office/excel=
/2003/xml" xmlns:ppda=3D"http://www.passport.com/NameSpace.xsd" xmlns:ois=
=3D"http://schemas.microsoft.com/sharepoint/soap/ois/" xmlns:dir=3D"http://=
schemas.microsoft.com/sharepoint/soap/directory/" xmlns:ds=3D"http://www.w3=
.org/2000/09/xmldsig#" xmlns:dsp=3D"http://schemas.microsoft.com/sharepoint=
/dsp" xmlns:udc=3D"http://schemas.microsoft.com/data/udc" xmlns:xsd=3D"http=
://www.w3.org/2001/XMLSchema" xmlns:sub=3D"http://schemas.microsoft.com/sha=
repoint/soap/2002/1/alerts/" xmlns:ec=3D"http://www.w3.org/2001/04/xmlenc#"=
 xmlns:sp=3D"http://schemas.microsoft.com/sharepoint/" xmlns:sps=3D"http://=
schemas.microsoft.com/sharepoint/soap/" xmlns:xsi=3D"http://www.w3.org/2001=
/XMLSchema-instance" xmlns:udcs=3D"http://schemas.microsoft.com/data/udc/so=
ap" xmlns:udcxf=3D"http://schemas.microsoft.com/data/udc/xmlfile" xmlns:udc=
p2p=3D"http://schemas.microsoft.com/data/udc/parttopart" xmlns:wf=3D"http:/=
/schemas.microsoft.com/sharepoint/soap/workflow/" xmlns:dsss=3D"http://sche=
mas.microsoft.com/office/2006/digsig-setup" xmlns:dssi=3D"http://schemas.mi=
crosoft.com/office/2006/digsig" xmlns:mdssi=3D"http://schemas.openxmlformat=
s.org/package/2006/digital-signature" xmlns:mver=3D"http://schemas.openxmlf=
ormats.org/markup-compatibility/2006" xmlns:m=3D"http://schemas.microsoft.c=
om/office/2004/12/omml" xmlns:mrels=3D"http://schemas.openxmlformats.org/pa=
ckage/2006/relationships" xmlns:spwp=3D"http://microsoft.com/sharepoint/web=
partpages" xmlns:ex12t=3D"http://schemas.microsoft.com/exchange/services/20=
06/types" xmlns:ex12m=3D"http://schemas.microsoft.com/exchange/services/200=
6/messages" xmlns:pptsl=3D"http://schemas.microsoft.com/sharepoint/soap/Sli=
deLibrary/" xmlns:spsl=3D"http://microsoft.com/webservices/SharePointPortal=
Server/PublishedLinksService" xmlns:Z=3D"urn:schemas-microsoft-com:" xmlns:=
st=3D"&#1;" xmlns=3D"http://www.w3.org/TR/REC-html40">

<head>
<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; charset=3Dus-ascii"=
>
<meta name=3DGenerator content=3D"Microsoft Word 12 (filtered medium)">
<style>
<!--
 /* Font Definitions */
 |font-face
	{font-family:"Cambria Math";
	panose-1:2 4 5 3 5 4 6 3 2 4;}
|font-face
	{font-family:Calibri;
	panose-1:2 15 5 2 2 2 4 3 2 4;}
|font-face
	{font-family:Consolas;
	panose-1:2 11 6 9 2 2 4 3 2 4;}
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{margin:0in;
	margin-bottom:.0001pt;
	font-size:11.0pt;
	font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
	{mso-style-priority:99;
	color:blue;
	text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
	{mso-style-priority:99;
	color:purple;
	text-decoration:underline;}
p.MsoPlainText, li.MsoPlainText, div.MsoPlainText
	{mso-style-priority:99;
	mso-style-link:"Plain Text Char";
	margin:0in;
	margin-bottom:.0001pt;
	font-size:10.5pt;
	font-family:Consolas;}
span.EmailStyle17
	{mso-style-type:personal-compose;
	font-family:"Calibri","sans-serif";
	color:windowtext;}
span.PlainTextChar
	{mso-style-name:"Plain Text Char";
	mso-style-priority:99;
	mso-style-link:"Plain Text";
	font-family:Consolas;}
.MsoChpDefault
	{mso-style-type:export-only;}
|page Section1
	{size:8.5in 11.0in;
	margin:1.0in 1.0in 1.0in 1.0in;}
div.Section1
	{page:Section1;}
-->
</style>
<!--[if gte mso 9]><xml>
 <o:shapedefaults v:ext=3D"edit" spidmax=3D"1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
 <o:shapelayout v:ext=3D"edit">
  <o:idmap v:ext=3D"edit" data=3D"1" />
 </o:shapelayout></xml><![endif]-->
</head>

<body lang=3DEN-US link=3Dblue vlink=3Dpurple>

<div class=3DSection1>

<p class=3DMsoPlainText>Dear Colleague,<o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>OpenEye's 11th annual CUP meeting will be held from
Monday, March 8th to Wednesday, March 10th, 2010 in Santa Fe, New Mexico at=
 the
Eldorado Hotel. The six sessions we intend to cover are:<o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>Monday morning: &quot;Practical Electrostatics - ho=
w far
do we have to go?&quot;<o:p></o:p></p>

<p class=3DMsoPlainText>--Evaluations of what the current state-of-the-art =
can
and can't calculate.<o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>Monday afternoon: &quot;Statistical reasoning in
molecular modeling&quot;<o:p></o:p></p>

<p class=3DMsoPlainText>--How best to use the information we have, whether =
> from
ligands, proteins or literature.<o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>Tuesday morning: &quot;Careful, that thing is loade=
d -
optimizing the interaction between Medicinal Chemistry and Modeling&quot; (=
Pat
Walters, guest organizer) --It doesn't matter how good your work is if the
chemists ignore it.<o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>Tuesday afternoon: &quot;MMPB: Panacea, useful or
useless?&quot;<o:p></o:p></p>

<p class=3DMsoPlainText>--Some rely on it, some find it useful and some can=
't get
anything out of it at all. Some leading lights will be asked to give their
opinion.<o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>Wednesday morning: &quot;Fragment-based Drug Discov=
ery:
Primary tool or tactic of last resort?&quot; <o:p></o:p></p>

<p class=3DMsoPlainText>--What and when is the appropriate use of FBDD?<o:p=
></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>Wednesday afternoon: &quot;New technology and old
dogs&quot;<o:p></o:p></p>

<p class=3DMsoPlainText>--Workflows, GPUs and clouds, oh my! Plus a round-t=
able:
&quot;Graphical scripting: Programming beyond our competence?&quot;<o:p></o=
:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>There is still room in some sessions for contribute=
d
talks - contact me if you are interested. Last year our Monday night poster
session was tremendous, so please think about contributing this way even if=
 you
don't think you can manage a talk. This year our Levinthal speaker will be =
Dr.
Ajay Jain from UCSF, who will present his talk: &quot;Molecular Evolution: =
The
Created and the Creators and the Puzzle of Design&quot;, after the Tuesday
afternoon session. &nbsp;And for the practically inclined, we are bookendin=
g
CUP with two technical sessions; one at 2pm on Sunday afternoon led by Bob
Tolbert on OE toolkits, and one starting at 9am on Thursday morning led by =
Joe
Corkery on adapting VIDA to enterprise-wide tasks.<o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>As always, there is no registration cost for CUP an=
d we
feed you Monday night at the posters and at the conference dinner Wednesday
night. To register for CUP 11, please go to:<o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText><a href=3D"http://www.eyesopen.com/forms/cup11_reg.=
html">http://www.eyesopen.com/forms/cup11_reg.html</a><o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>If you wish to stay at the conference hotel, please
contact the Eldorado Hotel, (<a href=3D"http://www.eldoradohotel.com">www.e=
ldoradohotel.com</a>,
505-988-4455). We have a block of rooms reserved so ask for the OpenEye rat=
e
($159) when making your reservation by phone or enter the special promotion=
s
code '247' if you use their website. Finally, in the last year American
Airlines has started operating daily flights between Santa Fe and Los Angel=
es
and Dallas/Fort Worth. Santa Fe airport is about a 15 minute taxi ride from
downtown.<o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>Look forward to seeing you there,<o:p></o:p></p>

<p class=3DMsoPlainText><o:p>&nbsp;</o:p></p>

<p class=3DMsoPlainText>Anthony<o:p></o:p></p>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

</div>

</body>

</html>

--_000_BB3CCF2D3D6B094D96588383620C5F3E4C7029DACFEXVMBX01811ex_--


From owner-chemistry@ccl.net Tue Dec  8 16:18:01 2009
From: "dipankar roy theodip : gmail.com" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL:G: Server system for Gaussian
Message-Id: <-40882-091208150922-5186-LyfSOwUtV2vChj9+FXN97g,server.ccl.net>
X-Original-From: dipankar roy <theodip|gmail.com>
Content-Type: multipart/alternative; boundary=001636c924beacae56047a3d2583
Date: Tue, 8 Dec 2009 15:09:10 -0500
MIME-Version: 1.0


Sent to CCL by: dipankar roy [theodip.:.gmail.com]
--001636c924beacae56047a3d2583
Content-Type: text/plain; charset=ISO-8859-1

Hi,
Please configure as per your requirements based on:
(i) size of the molecular systems you will analyze,
(ii) type of calculation (DFT will be fine with those configurations you
mentioned but post-HF may cause trouble)

hope that will help,
regards,
Dipankar

On Tue, Dec 8, 2009 at 1:17 PM, Serdar Badoglu sbadoglu]![gazi.edu.tr <
owner-chemistry!^!ccl.net> wrote:

>
> Sent to CCL by: "Serdar  Badoglu" [sbadoglu()gazi.edu.tr]
> Dear CCLers,
>
> We are intended to buy a server system to do our Gaussian calculations, and
> we are planning to expand our hardware in the future. As a start, we have
> collected several proposals from companies. First of all, I wonder if the
> below cheap systems are good or not for computational uses:
>
> 1- HP DL160G6 with two quad core CPUs, 4GB memory and 160GB HDD
> 2- HP DL380G6 with two quad core CPUs, 4GB memory and 2 x 146GB HDD
> 3- Fujitsu-Siemens system (content is not clear yet)
>
> Besides I'd like to know what kind of servers you use in your calculations.
> As experienced users, what would you suggest us?
>
> Regards.>
>
>

--001636c924beacae56047a3d2583
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Hi,<br>Please configure as per your requirements based on:<br>(i) size of t=
he molecular systems you will analyze,<br>(ii) type of calculation (DFT wil=
l be fine with those configurations you mentioned but post-HF may cause tro=
uble)<br>
<br>hope that will help,<br>regards,<br>Dipankar <br><br><div class=3D"gmai=
l_quote">On Tue, Dec 8, 2009 at 1:17 PM, Serdar Badoglu sbadoglu]![<a href=
=3D"http://gazi.edu.tr">gazi.edu.tr</a> <span dir=3D"ltr">&lt;<a href=3D"ma=
ilto:owner-chemistry!^!ccl.net">owner-chemistry!^!ccl.net</a>&gt;</span> wrote:=
<br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: &quot;Serdar =A0Badoglu&quot; [sbadoglu()<a href=3D"http://=
gazi.edu.tr" target=3D"_blank">gazi.edu.tr</a>]<br>
Dear CCLers,<br>
<br>
We are intended to buy a server system to do our Gaussian calculations, and=
 we are planning to expand our hardware in the future. As a start, we have =
collected several proposals from companies. First of all, I wonder if the b=
elow cheap systems are good or not for computational uses:<br>

<br>
1- HP DL160G6 with two quad core CPUs, 4GB memory and 160GB HDD<br>
2- HP DL380G6 with two quad core CPUs, 4GB memory and 2 x 146GB HDD<br>
3- Fujitsu-Siemens system (content is not clear yet)<br>
<br>
Besides I&#39;d like to know what kind of servers you use in your calculati=
ons. As experienced users, what would you suggest us?<br>
<br>
Regards.<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
<br>
E-mail to subscribers: <a href=3D"mailto:CHEMISTRY!^!ccl.net">CHEMISTRY!^!ccl.n=
et</a> or use:<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" tar=
get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST!^!ccl.net">CHEM=
ISTRY-REQUEST!^!ccl.net</a> or use<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" tar=
get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
Subscribe/Unsubscribe:<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtml" target=
=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br>
Job: <a href=3D"http://www.ccl.net/jobs" target=3D"_blank">http://www.ccl.n=
et/jobs</a><br>
Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe=
rences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/co=
nferences/</a><br>
<br>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
a><br>
<br<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank">h=
ttp://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</blockquote></div><br>

--001636c924beacae56047a3d2583--


From owner-chemistry@ccl.net Tue Dec  8 16:58:00 2009
From: "Daniel Jana dfjana===gmail.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL:G: Server system for Gaussian
Message-Id: <-40883-091208142757-1613-wORMidbOg89x68GKgoWrKw#,#server.ccl.net>
X-Original-From: Daniel Jana <dfjana%a%gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Tue, 08 Dec 2009 20:27:26 +0100
MIME-Version: 1.0


Sent to CCL by: Daniel Jana [dfjana..gmail.com]
Hello,

Serdar Badoglu sbadoglu]![gazi.edu.tr wrote:
> Sent to CCL by: "Serdar  Badoglu" [sbadoglu()gazi.edu.tr]
> Dear CCLers, 
>
> We are intended to buy a server system to do our Gaussian calculations, and we are planning to expand our hardware in the future. As a start, we have collected several proposals from companies. First of all, I wonder if the below cheap systems are good or not for computational uses:
>
> 1- HP DL160G6 with two quad core CPUs, 4GB memory and 160GB HDD
> 2- HP DL380G6 with two quad core CPUs, 4GB memory and 2 x 146GB HDD
> 3- Fujitsu-Siemens system (content is not clear yet)
>   

I'm not sure which kind of calculations you are trying to do mainly 
(classical MD, DFT, high level ab initio methods) and that does make a 
difference on the type of hardware to buy.
However, I'd say that you have too little memory. Having two quad core 
cpus means you will have a total of 8 cores to run calculations and with 
only 4 GB you have an average of 500 MB per core. While that may be good 
for what you intend to do, if you plan on doing coupled cluster or 
something similar it will definitely not be enough. I'd say the minimum 
nowadays would be 1 GB per core, perhaps 2 GB if you can afford it. If 
you are going to do MP2 and above stuff I would then recommend 4 GB per 
core (if you can't afford that, I'd then invest on buying the memory in 
only a single DIMM (or two, for dual channel purposes) so that you can 
buy more later on. Saving money by buying 4x1GB RAM will be bad on the 
long run).

As for the disk... once again it depends on the computations you are 
going to do and the way you will be using the servers. Will you try to 
use as much as possible 8 cpu jobs? Or do you think you'll have lots of 
1 or 2 cpu jobs? If you run mainly 8 cpu jobs then it should be fine 
with one disk (you may want to have a bigger size though, if you plan on 
doing stuff that stores a lot of integrals [once again, high level ab 
initio stuff]). If you are going to run several jobs per machine I think 
you should try two disks as the I/O may become an even bigger problem 
that what it usually is (if different jobs are trying to access 
different parts of the disk you'll get lower performance).

Hope this helps and if you could tell us a bit more about the kind of 
calculation you'll be running, perhaps other people will have a better 
insight.

Cheers,
Daniel


From owner-chemistry@ccl.net Tue Dec  8 17:28:01 2009
From: "Serdar Bado?lu sbadoglu .. gazi.edu.tr" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: Server system for Gaussian
Message-Id: <-40884-091208154821-10690-q4FDFhQhG0FXpa+wXfOsug^^^server.ccl.net>
X-Original-From: "Serdar Bado?lu" <sbadoglu=-=gazi.edu.tr>
Date: Tue, 8 Dec 2009 20:17:03 -0000


Sent to CCL by: "Serdar Bado?lu" [sbadoglu^-^gazi.edu.tr]
Meanwhile Daniel Jana warned me about something. Thank you Daniel.

I'd better tell you something about our calculations, so you can comment
better.

Up to now we carried out our calculations on ordinary desktop PCs. Our
routine calculations are on molecules containing 20-25 atoms.
Optimization, frequency, energy, NMR, charge calculations; and the same
for complexes and dimers of the free ligand. Most of the time our
calculation level is B3LYP/6-311++G** for the free ligand, nowadays we
tend to use cc-pVxZ sets for energy calculations, MP2 rarely used at the
moment. Our plan is to work on larger molecules and/or we plan to do
higher level of calculations.

Regards.


From owner-chemistry@ccl.net Tue Dec  8 18:04:01 2009
From: "Loriann Monsier lmonsier===chemcomp.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: CCG Releases MOE 2009.10 Today
Message-Id: <-40885-091208171809-24063-njH0pmGbMe1Dg9Fnm0v9ww_._server.ccl.net>
X-Original-From: "Loriann  Monsier" <lmonsier()chemcomp.com>
Date: Tue, 8 Dec 2009 17:18:05 -0500


Sent to CCL by: "Loriann  Monsier" [lmonsier ~ chemcomp.com]
Chemical Computing Group Inc. Releases New Version of the Molecular Operating Environment 

MONTREAL, December 08, 2009 -- Chemical Computing Group Inc. (CCG) announces the general release of the 2009.10 version of the Molecular Operating Environment (MOE).  The 2009 release contains new technology for:

* Real-time ray-traced graphics including full screen anti-aliasing focal
  blur effects taking advantage of modern graphic cards to create 
  ray-traced images at interactive speeds.

* Scaffold replacement and linking for ligand- or structure-based design
  projects.

* SOAP server to integrate MOE into pipeline workflows. It offers
  flexibility to use MOE as a web service from external programs or
  web pages.

* LowModeMD conformational search of protein loops and complex systems.
  It combines combines molecular dynamics and conformational analysis
  to explore the structural variations of complex molecular systems.

* Synthetic Score descriptor to estimate synthetic feasibility of
  virtual compounds.

* Protein/Antibody Modeling technology for enhanced backbone and
  sidechain sampling.

CCG (http://www.chemcomp.com) headquartered in Montreal, Canada, is a leading supplier of software solutions for Life Sciences. Please visit our web site for comprehensive information about all our products.

For additional information please contact:
Elizabeth Sourial, Director of Scientific Services
(514) 393-1055
esourial^_^chemcomp.com or info^_^chemcomp.com


From owner-chemistry@ccl.net Tue Dec  8 22:32:00 2009
From: "jean-francois prieur jfprieur..@..gmail.com" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Server system for Gaussian
Message-Id: <-40886-091208183737-25631-Y+BcEPFgVlzS+g+aYwPsLQ.@.server.ccl.net>
X-Original-From: jean-francois prieur <jfprieur^-^gmail.com>
Content-Type: multipart/alternative; boundary=0016e6d999e15b16ba047a400efd
Date: Tue, 8 Dec 2009 18:37:04 -0500
MIME-Version: 1.0


Sent to CCL by: jean-francois prieur [jfprieur#,#gmail.com]
--0016e6d999e15b16ba047a400efd
Content-Type: text/plain; charset=ISO-8859-1

If you plan a higher basis set/theory, i would say that the disk space in
the servers you listed will not be sufficient. The 'smallest' server hard
drive I see nowadays is 500GB, they are not that expensive and is the
minimum spec I would put in a server dedicated to calculations. You could
probably get away with 250GB if your budget is limited.

Regards,
JF Prieur

2009/12/8 Serdar Bado?lu sbadoglu .. gazi.edu.tr <owner-chemistry\a/ccl.net>

>
> Sent to CCL by: "Serdar Bado?lu" [sbadoglu^-^gazi.edu.tr]
> Meanwhile Daniel Jana warned me about something. Thank you Daniel.
>
> I'd better tell you something about our calculations, so you can comment
> better.
>
> Up to now we carried out our calculations on ordinary desktop PCs. Our
> routine calculations are on molecules containing 20-25 atoms.
> Optimization, frequency, energy, NMR, charge calculations; and the same
> for complexes and dimers of the free ligand. Most of the time our
> calculation level is B3LYP/6-311++G** for the free ligand, nowadays we
> tend to use cc-pVxZ sets for energy calculations, MP2 rarely used at the
> moment. Our plan is to work on larger molecules and/or we plan to do
> higher level of calculations.
>
> Regards.>
>
>

--0016e6d999e15b16ba047a400efd
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

If you plan a higher basis set/theory, i would say that the disk space in t=
he servers you listed will not be sufficient. The &#39;smallest&#39; server=
 hard drive I see nowadays is 500GB, they are not that expensive and is the=
 minimum spec I would put in a server dedicated to calculations. You could =
probably get away with 250GB if your budget is limited.<div>

<br></div><div>Regards,</div><div>JF Prieur<br><br><div class=3D"gmail_quot=
e">2009/12/8 Serdar Bado?lu sbadoglu .. <a href=3D"http://gazi.edu.tr">gazi=
.edu.tr</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry\a/ccl.net=
">owner-chemistry\a/ccl.net</a>&gt;</span><br>

<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;"><br>
Sent to CCL by: &quot;Serdar Bado?lu&quot; [sbadoglu^-^<a href=3D"http://ga=
zi.edu.tr" target=3D"_blank">gazi.edu.tr</a>]<br>
Meanwhile Daniel Jana warned me about something. Thank you Daniel.<br>
<br>
I&#39;d better tell you something about our calculations, so you can commen=
t<br>
better.<br>
<br>
Up to now we carried out our calculations on ordinary desktop PCs. Our<br>
routine calculations are on molecules containing 20-25 atoms.<br>
Optimization, frequency, energy, NMR, charge calculations; and the same<br>
for complexes and dimers of the free ligand. Most of the time our<br>
calculation level is B3LYP/6-311++G** for the free ligand, nowadays we<br>
tend to use cc-pVxZ sets for energy calculations, MP2 rarely used at the<br=
>
moment. Our plan is to work on larger molecules and/or we plan to do<br>
higher level of calculations.<br>
<br>
Regards.<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
<br>
E-mail to subscribers: <a href=3D"mailto:CHEMISTRY\a/ccl.net">CHEMISTRY\a/ccl.n=
et</a> or use:<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" tar=
get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST\a/ccl.net">CHEM=
ISTRY-REQUEST\a/ccl.net</a> or use<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" tar=
get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
Subscribe/Unsubscribe:<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtml" target=
=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br>
Job: <a href=3D"http://www.ccl.net/jobs" target=3D"_blank">http://www.ccl.n=
et/jobs</a><br>
Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe=
rences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/co=
nferences/</a><br>
<br>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
a><br>
<br<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank">h=
ttp://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</blockquote></div><br></div>

--0016e6d999e15b16ba047a400efd--


From owner-chemistry@ccl.net Tue Dec  8 23:10:01 2009
From: "Tsung-Wen Yen peter308:-:gmail.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: What's the reasonable range for Mulliken charges on metallic cluster?
Message-Id: <-40887-091208225522-6975-YnMH7SrytD1H++CQ9PnXyA-x-server.ccl.net>
X-Original-From: "Tsung-Wen  Yen" <peter308]![gmail.com>
Date: Tue, 8 Dec 2009 22:55:18 -0500


Sent to CCL by: "Tsung-Wen  Yen" [peter308(~)gmail.com]
Dear CClers:
My caluculation of Mulliken partial charge on noble metallic clusters(N=38)
has some peculiar results. Some of the atoms will show 5~6 electrons. Is this reasonable? I used (RECP19|SD) basis set for Gold and Copper. Could you tell me on which range should be reasonable for MPA charges? I have the feeling my electron structure may have converged to a wrong state. I appreciated for your advice.


                                          Best Regards
                                          Tsung-Wen Yen