From owner-chemistry@ccl.net Thu Nov 22 05:40:00 2012 From: "uekstrom{=}gmail.com uekstrom{=}gmail.com" To: CCL Subject: CCL: Need advice on buying a large memory pc Message-Id: <-47893-121122053759-21012-R5yhVjSN3QD3cGxMFS2cAA[a]server.ccl.net> X-Original-From: "uekstrom!A!gmail.com" Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Nov 2012 11:37:53 +0100 MIME-Version: 1.0 Sent to CCL by: "uekstrom.:.gmail.com" [uekstrom.:.gmail.com] Dear all, I want to buy a pc with a lot of memory. I see that HP, Dell etc offer machines that can take up to 256GB memory. I indend to run some sort of Linux on the machine, which will mainly be used for correlated calculations. Three questions: Is it worth going for ECC memory? How common are memory errors anyway? Is there any special motherboard I should avoid (for Intel Xeon CPUs)? Does modern Linux run efficiently out of the box with 256 GB memory? I remember there were some patches for extra large pages that were needed in the past, but now I imagine this amount of memory is not so uncommon anymore. Regards, Ulf Ekstrom, University of Oslo From owner-chemistry@ccl.net Thu Nov 22 06:33:00 2012 From: "Pedro Silva pedros/a\ufp.edu.pt" To: CCL Subject: CCL: Article on Structural realism in Chemistry in latest New Scientist Message-Id: <-47894-121122063111-11127-gckD6xZjvny/y/GQs9Dd1g++server.ccl.net> X-Original-From: Pedro Silva Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Nov 2012 11:31:05 +0000 MIME-Version: 1.0 Sent to CCL by: Pedro Silva [pedros(-)ufp.edu.pt] Let's all start to publicize our papers on CCL: a captive audience JUST waiting to know about our unrequested pearls of wisdom! Yipee! Should we realy have to put up with unrequested publicity, in exchange for an opportunity to discuss tips and knowledge with our colleagues? Isn't there enough spam floating around already? Pedro S. -- Pedro J. Silva Associate Professor Universidade Fernando Pessoa Porto - Portugal http://homepage.ufp.pt/pedros/science/science.htm http://biochemicalmatters.blogspot.com From owner-chemistry@ccl.net Thu Nov 22 07:08:00 2012 From: "Alcides Simao alsimao(0)gmail.com" To: CCL Subject: CCL: Need advice on buying a large memory pc Message-Id: <-47895-121122070125-30931-cMw7IeFldX/VvJnlzQbL5w(_)server.ccl.net> X-Original-From: Alcides Simao Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Nov 2012 13:01:16 +0100 MIME-Version: 1.0 Sent to CCL by: Alcides Simao [alsimao=gmail.com] Hi Ülf! As far as EEC memory is concerned, I don't think it to be necessary. But, if you need a second opinion... http://www.crucial.com/kb/answer.aspx?qid=3692 and http://www.tomshardware.co.uk/forum/221285-12-memory As far as mobo's are concerned, I can't give you an expert opinion, and, moreover, I don't use server-grade equipment. What I can tell you, from my humble experience, is that Intel equipment (mobo's, ethernet cards, etc) handle stress much better that other vendors. I recall having many problems with realtek and atheros onboard LAN, which kept crashing when I attempted to paralelize the cluster at the lab. Switched them to Intel cards and they worked flawlessly. But it might be a wrong impression. As for the 256 GB ram issue, please see here http://linuxhardware.net/linuxhardware/notes/ It should be listed. Also, I would suggest you to take some time and read this pages - you might find them relevant! http://www.sharkyforums.com/showthread.php?320718-New-Linux-system-4x-Octal-Core-Xeon-s-256GB-RAM http://serverfault.com/questions/15636/cost-effective-way-to-build-a-server-with-lots-of-ram From owner-chemistry@ccl.net Thu Nov 22 09:25:00 2012 From: "Prof. Dr. N. Sekar nethi.sekar^gmail.com" To: CCL Subject: CCL: Article on Structural realism in Chemistry in latest New Scientist Message-Id: <-47896-121122092225-19425-brHM4v3hqaY3la6FPoigMg.:.server.ccl.net> X-Original-From: "Prof. Dr. N. Sekar" Content-Type: multipart/alternative; boundary=e89a8f502e0c998d9c04cf1631da Date: Thu, 22 Nov 2012 19:52:15 +0530 MIME-Version: 1.0 Sent to CCL by: "Prof. Dr. N. Sekar" [nethi.sekar=-=gmail.com] --e89a8f502e0c998d9c04cf1631da Content-Type: text/plain; charset=ISO-8859-1 Dear Prof Eric, Please send me soft copy of your article. On Thu, Nov 22, 2012 at 5:01 PM, Pedro Silva pedros/aufp.edu.pt < owner-chemistry _ ccl.net> wrote: > > Sent to CCL by: Pedro Silva [pedros(-)ufp.edu.pt] > > > Let's all start to publicize our papers on CCL: a captive audience > JUST waiting to know about our unrequested pearls of wisdom! > > Yipee! > > > > Should we realy have to put up with unrequested publicity, in exchange > for an opportunity to discuss tips and knowledge with our colleagues? > Isn't there enough spam floating around already? > > Pedro S. > > > > -- > Pedro J. Silva > Associate Professor > Universidade Fernando Pessoa > Porto - Portugal > http://homepage.ufp.pt/pedros/science/science.htm > http://biochemicalmatters.blogspot.com> > > -- Thanks and regards Prof. Dr. N. Sekar CCol FSDC Head, Department of Dyestuff Technology Co-ordinator, UGC-CAS and Professor in Tinctorial Chemistry Institute of Chemical Technology (formerly UDCT) Matunga, Mumbai-400019 Mob +91-9867958452 n.sekar _ ictmumbai.edu.in website: http://ictmumbai.edu.in/Fac_FacDetails.aspx?fidno=116 --e89a8f502e0c998d9c04cf1631da Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Prof Eric,
Please send me soft copy of your article.

On Thu, Nov 22, 2012 at 5:01 PM, Pedro Silva pedros/aufp.edu.pt <owner-chemistry _ ccl.n= et> wrote:

Sent to CCL by: Pedro Silva [pedros(-)ufp.edu.pt]
<sarcasm>

Let's all start to publicize our papers on CCL: a captive audience
JUST waiting to know about our unrequested pearls of wisdom!

Yipee!

</sarcasm>

Should we realy have to put up with unrequested publicity, in exchange
for an opportunity to discuss tips and knowledge with our colleagues?
Isn't there enough spam floating around already?

Pedro S.



--
Pedro J. Silva
Associate Professor
Universidade Fernando Pessoa
Porto - Portugal
http://homepage.ufp.pt/pedros/science/science.htm
http:/= /biochemicalmatters.blogspot.com



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Thanks = and regards

Prof. Dr. N. Sekar=A0=A0 CCol FSDC
Head, Department o= f Dyestuff Technology
Co-ordinator, UGC-CAS and Professor in Tinc= torial Chemistry
Institute of Chemical Technology (formerly UDCT)
Matunga, Mumbai-400019<= br>
Mob +91-9867958452
n.sekar _ ictmumbai.edu.in
=A0

--e89a8f502e0c998d9c04cf1631da-- From owner-chemistry@ccl.net Thu Nov 22 13:21:00 2012 From: "Jussi Lehtola jussi.lehtola^helsinki.fi" To: CCL Subject: CCL: Need advice on buying a large memory pc Message-Id: <-47897-121122063556-14069-+vylA6+JLTkZrey/vSKEhg..server.ccl.net> X-Original-From: Jussi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 22 Nov 2012 13:35:44 +0200 Mime-Version: 1.0 Sent to CCL by: Jussi Lehtola [jussi.lehtola+*+helsinki.fi] On Thu, 22 Nov 2012 11:37:53 +0100 "uekstrom{=}gmail.com uekstrom{=}gmail.com" wrote: > Sent to CCL by: "uekstrom.:.gmail.com" [uekstrom.:.gmail.com] > Dear all, > I want to buy a pc with a lot of memory. I see that HP, Dell etc offer > machines that > can take up to 256GB memory. I indend to run some sort of Linux on > the machine, which will mainly be used for correlated calculations. > Three questions: > > Is it worth going for ECC memory? How common are memory errors anyway? > > Is there any special motherboard I should avoid (for Intel Xeon > CPUs)? > > Does modern Linux run efficiently out of the box with 256 GB memory? I > remember there were some patches for extra large pages that were > needed in the past, but now I imagine this amount of memory is not so > uncommon anymore. Our university recently bought a cluster with one node that has 1 TB of memory, so that the whole genome can be fitted into the RAM. The machine is running a stock RHEL 6 kernel (i.e., Scientific Linux 6.3). So I'd say yes. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.lehtola,+,helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.lehtola,+,helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- From owner-chemistry@ccl.net Thu Nov 22 13:56:00 2012 From: "Alex A. Granovsky gran[*]classic.chem.msu.su" To: CCL Subject: CCL: Good reviews on LIMS systems? Message-Id: <-47898-121122093125-21831-pGbSzx1IfkpXZNTAgzC1FQ]![server.ccl.net> X-Original-From: "Alex A. Granovsky" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0484_01CDC8DF.6F6366E0" Date: Thu, 22 Nov 2012 18:30:23 +0400 MIME-Version: 1.0 Sent to CCL by: "Alex A. Granovsky" [gran- -classic.chem.msu.su] This is a multi-part message in MIME format. ------=_NextPart_000_0484_01CDC8DF.6F6366E0 Content-Type: text/plain; charset="utf-7" Content-Transfer-Encoding: quoted-printable Dear CCLers, I would be very grateful if someone could suggest good critical reviews = on modern LIMS systems. Kind regards, Alex Granovsky ------=_NextPart_000_0484_01CDC8DF.6F6366E0 Content-Type: text/html; charset="utf-7" Content-Transfer-Encoding: quoted-printable +ADw-HTML+AD4APA-HEAD+AD4APA-/HEAD+AD4- +ADw-BODY dir+AD0-ltr+AD4- +ADw-DIV dir+AD0-ltr+AD4- +ADw-DIV style+AD0AIg-FONT-FAMILY: 'Calibri'+ADs- COLOR: = +ACM-000000+ADs- FONT-SIZE: 12pt+ACIAPg- +ADw-DIV+AD4-Dear CCLers,+ADw-/DIV+AD4- +ADw-DIV+AD4AJg-nbsp+ADsAPA-/DIV+AD4- +ADw-DIV+AD4-I would be very grateful if someone could suggest good = critical reviews on=20 modern LIMS systems.+ADw-/DIV+AD4- +ADw-DIV+AD4AJg-nbsp+ADsAPA-/DIV+AD4- +ADw-DIV+AD4-Kind regards,+ADw-/DIV+AD4- +ADw-DIV+AD4-Alex = Granovsky+ADw-/DIV+AD4APA-/DIV+AD4APA-/DIV+AD4APA-/BODY+AD4APA-/HTML+AD4-= ------=_NextPart_000_0484_01CDC8DF.6F6366E0-- From owner-chemistry@ccl.net Thu Nov 22 14:31:00 2012 From: "Adam Langlois Adam.Langlois%x%USherbrooke.ca" To: CCL Subject: CCL:G: DFT Methods For Intermolecular Pi-Pi Interactions Message-Id: <-47899-121122104841-1369-w4tUXVfBNyCTL+PbHV8l4A],[server.ccl.net> X-Original-From: "Adam Langlois" Date: Thu, 22 Nov 2012 10:48:40 -0500 Sent to CCL by: "Adam Langlois" [Adam.Langlois||USherbrooke.ca] I have been assigned a calculations project where I am asked to do a DFT calculations to optimise the geometry of a porphyrin triamer and hexamer that interact through Pi-Pi interactions with C60. The interaction is a "ball-in- glove" type of interaction where there is an overlap of the Pi orbitals of the porphyrin rings and the Pi orbitals of the C60. My question is what DFT method is best suited for this type of calculation? For most of the calculations that I have carried out in the past I have used the B3LYP method. However, I have heard that this is not the best method for long-distance or intermolecular interactions. I have been told about two other methods that may be useful in a situation like this. The first is the CAM-B3LYP method which is supposed to take long distance interactions into account. However, I have recently compared the CAM-B3LYP method to the B3LYP method in calculations that involved a co- facial special pair of porphyrin and found that the B3LYP method better represented that experimental data. I have also heard of the a method known as the M05-2X functional, which is supposed to another good method for long distance interactions such as hydrogen bonding. However, I do not see this functional as an option in the Gaussian calculation set-up window. A second question is with regard to the basis sets. I plan on using the ONIOM method to save on computation time. I plan on applying the PM6 method as a low level and a DFT method as a high level. However I am not sure how large of a basis set I should use. Normally I carry out my calculations with a 6-31G* basis set. Is this large enough to take into account the intermolecular interactions or go I need to employ a more disperse basis set such as 6-311g++. A paper that I found used a 6-311g++(2df,2dp) basis set to examine intermolecular hydrogen bonding which is a large, and very disperse basis set. However, the paper also modelled very small structures. Any suggestions for basis sets here would be appreciated. Finally, once I have modelled the triamer and the hexamer without C60 I will need to model them with C60. Where again I will employ the ONIOM method. My question here is, do I include the C60 in my high layer or my low layer? I would like to thank you in advance for all of your help. Adam Langlois Universite de Sherbooke Quebec Canada Adam.Langlois*o*USherbrooke.ca From owner-chemistry@ccl.net Thu Nov 22 15:06:00 2012 From: "Igor Filippov igor.v.filippov::gmail.com" To: CCL Subject: CCL: Need advice on buying a large memory pc Message-Id: <-47900-121122115625-12712-ixPLuTfP7E5FHLWRJsTFxQ-,-server.ccl.net> X-Original-From: Igor Filippov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Thu, 22 Nov 2012 11:56:32 -0500 Mime-Version: 1.0 Sent to CCL by: Igor Filippov [igor.v.filippov(a)gmail.com] You can purchase this kind of system from PenguinComputing and it will come configured with Linux. I can't say for 256Gb but we have purchased 192Gb RAM systems from them before. Modern Linux works fine there, no special configuration required. http://www.penguincomputing.com/Products/RackmountedServers/Relion/Relion1800 I personally would avoid anything from Dell. Cheap stuff is cheap there but anything more sophisticated is rather overpriced. If you need something cheaper you can get a 64Gb Sandy Bridge E system > from cyberpower. You'd have to install Linux yourself though in that case. I got a very nice 64Gb RAM workstation for under $2,500 there. http://www.cyberpowerpc.com/system/CyberPower_X79_Configurator Igor On Thu, 2012-11-22 at 11:37 +0100, uekstrom{=}gmail.com uekstrom{=}gmail.com wrote: > Sent to CCL by: "uekstrom.:.gmail.com" [uekstrom.:.gmail.com] > Dear all, > I want to buy a pc with a lot of memory. I see that HP, Dell etc offer > machines that > can take up to 256GB memory. I indend to run some sort of Linux on the machine, > which will mainly be used for correlated calculations. Three questions: > > Is it worth going for ECC memory? How common are memory errors anyway? > > Is there any special motherboard I should avoid (for Intel Xeon > CPUs)? > > Does modern Linux run efficiently out of the box with 256 GB memory? I > remember there were some patches for extra large pages that were > needed in the past, but now I imagine this amount of memory is not so > uncommon anymore. > > Regards, > Ulf Ekstrom, University of Oslo> > From owner-chemistry@ccl.net Thu Nov 22 15:41:00 2012 From: "Johannes Johansson johjo76|a|gmail.com" To: CCL Subject: CCL: Article on Structural realism in Chemistry in latest New Scientist Message-Id: <-47901-121122135659-19292-7u0kp1KZxRyA3AyGFxabCw_-_server.ccl.net> X-Original-From: Johannes Johansson Content-Type: multipart/alternative; boundary=20cf3074b554c94e9804cf1a075c Date: Thu, 22 Nov 2012 19:56:53 +0100 MIME-Version: 1.0 Sent to CCL by: Johannes Johansson [johjo76+/-gmail.com] --20cf3074b554c94e9804cf1a075c Content-Type: text/plain; charset=UTF-8 Dear Eric, I would be happy to receive a copy of your article. Thank you in advance! / Johannes -- Adam Johannes Johansson Ph.D., M.Sc. Linkedin: http://se.linkedin.com/pub/adam-johannes-johansson/22/209/395 ************************************************************************************** Read the biography: Inga Fischer-Hjalmars (1918-2008) - Swedish Pharmacist, Humanist and Pioneer Quantum Chemist: http://pubs.acs.org/doi/abs/10.1021/ed300024g ************************************************************************************** --20cf3074b554c94e9804cf1a075c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Eric,

I would be happy to receive a copy of your ar= ticle.

Thank you in advance! / Johannes

-- =
Adam Johannes Johansson
Ph.D., M.Sc.
Linkedin: h= ttp://se.linkedin.com/pub/adam-johannes-johansson/22/209/395
***************************************************************************= ***********
Read the biography: Inga Fischer-Hjalmars (1918-2008) - Swed= ish Pharmacist, Humanist and Pioneer Quantum Chemist: http://pubs.acs.org/= doi/abs/10.1021/ed300024g
***************************************************************************= ***********





--20cf3074b554c94e9804cf1a075c-- From owner-chemistry@ccl.net Thu Nov 22 16:33:01 2012 From: "Raul Alvarez ralvarez_._chemcomp.com" To: CCL Subject: CCL: CCG releases MOE 2012.10 with an expanded set of biologics applications Message-Id: <-47902-121122162543-15491-L/mQ0NfAWi3vlw8ssjhfsw-$-server.ccl.net> X-Original-From: "Raul Alvarez" Content-Language: en-us Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 22 Nov 2012 16:25:35 -0500 MIME-Version: 1.0 Sent to CCL by: "Raul Alvarez" [ralvarez:-:chemcomp.com] We are pleased to announce the release of MOE 2012.10. This latest version of MOE includes new applications focused on protein engineering and biologics tools as well as new enhancements in the areas of usability, force field development and reaction-based combinatorial library enumeration. More about MOE’s integrated biologics applications at http://www.chemcomp.com/software-biologics.htm. For additional information or to request a free trial of MOE 2012.10, please contact: Raul Alvarez, Sr. Marketing Manager, ralvarez!=!chemcomp.com =============================================================== NEW & ENHANCED FEATURES IN MOE 2012.10 =============================================================== *Integrated Protein Engineering Applications* - Residue scanning to identify critical residues for affinity - Search for optimal mutations to modulate thermostability - Predict hydrophobic and electrostatic hot spots with the protein Patch Analyzer *Domain Motif Searching* - Compare protein domains based on secondary structure elements - Search proteins for secondary structure sub-geometries - Identify similarities independent of sequence *Amber12:EHT: New Force Field for Biopolymers and Small Molecules* - Amber12 parameters for proteins and nucleic acids - Extended Hückel Theory parameterization of small molecules - More precise treatment of resonance and substituent effects *Reaction-based Library Enumeration and Screening* - New reaction engine combined with library enumeration or sampling - Sketch reactions or core/R-group libraries - Screen products with 2D or 3D filters (educts & products) *Usability Enhancements* - Docked System Manager with control over surfaces - Undo, redo, keyboard shortcuts, configurable mouse, drag & drop, etc. - 2D sketcher integration with MOE Window =============================================================== MOE MAIN APPLICATION AREAS: http://www.chemcomp.com/software.htm Structure-Based Design | Fragment-Based Design | Pharmacophore Discovery | Biologics & Protein Modeling | QSAR & HTS Cheminformatics | Medicinal Chemistry Design =============================================================== Read/download the official MOE 2012.10 press release at http://www.chemcomp.com/press_releases/2012-11-21-MOE2012.10.pdf From owner-chemistry@ccl.net Thu Nov 22 23:37:01 2012 From: "Savita Pundlik savita.pundlik(-)tcs.com" To: CCL Subject: CCL: Article on Structural realism in Chemistry in latest New Scientist Message-Id: <-47903-121122224600-8178-sF/Z4oayBIqknzUNeK1vzg]|[server.ccl.net> X-Original-From: Savita Pundlik Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="iso-8859-1" Date: Fri, 23 Nov 2012 09:15:45 +0530 MIME-Version: 1.0 Sent to CCL by: Savita Pundlik [savita.pundlik###tcs.com]
Hello,
 
Request you to kindly send me a copy of your article.
 
Thanks and Regards,
 
Savita Pundlik=
Tata Consultancy Services
Mailto: savita.pundlik,tcs.com
Website: http://www.tcs.com


-----owner-chemistry+savita.pundlik=3D=3Dtcs.com,ccl.net wrote: = ----- =
To: "Pundlik, Savita Su= nil " <savita.pundlik,tcs.com>
From: "Eric Scerri scerri##= chem.ucla.edu"
Sent by: owner-chemistry+savita= .pundlik=3D=3Dtcs.com,ccl.net
Date: 11/22/2012 10:02AM
Subject: CCL: = Article on Structural realism in Chemistry in latest New Scientist

<= !--Notes ACF = -->please see, =


full article available on request.
        = =

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