From owner-chemistry@ccl.net Wed Jun 23 00:01:00 2010 From: "Michael Krein kreinm2!A!rpi.edu" To: CCL Subject: CCL: Linux operating system Message-Id: <-42149-100622214819-5572-IswKAodyLVcrj0lj7gdZkg]_[server.ccl.net> X-Original-From: Michael Krein Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 22 Jun 2010 21:48:10 -0400 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Michael Krein [kreinm2**rpi.edu] Adel, It's a bit difficult to give a recommendation based on the information provided. Could you be more specific in what you wish to accomplish and in what software you're planning on using? How familiar with Linux/Unix systems are the people that are planning on using/maintaining the hardware? Do they have a preference? Assuming that there are no specific requirements, it's also very possible to pick the cheapest solution (Which may even be Windows), and clean install a *free* Linux install over what came preinstalled. Some colleagues swear by Ubuntu ( http://www.ubuntu.com/ ), which is easy to manage, but is somewhat bleeding-edge. I tend toward CentOS (http://www.centos.org/ ), which is, for all intents and purposes, identical to Red Hat, but is free of charge. As for file compatibility, I've never noticed any problems, though there are the unix commandline utilities 'unix2dos' and 'dos2unix' that will do the job. Cheers, -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- Michael Krein Breneman Research Group Rensselaer Exploratory Center for Cheminformatics Research Rensselaer Polytechnic Institute -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- On Jun 22, 2010, at 7:10 PM, Adel El-Azhary azhary+/-ksu.edu.sa wrote: > > Sent to CCL by: "Adel El-Azhary" [azhary.:.ksu.edu.sa] > Dear CCL members. > > We are planning to buy a dell power server with two Xeon processors. There are three options of the operating system. Does anyone have a preference for any of them, other than the price? The three operating systems are: > > 1. Red Hat Enterprise Linux 5.3, 2S, FI x64, 3yr, Auto-Entitle, Lic & Media [$1,099.00]. > 2. SUSE Linux Enterprise Server 11, 1-2CPU, 3 YR Subscription, FI, Media [$349.00]. > 3. SUSE Linux Enterprise Server 10, SP3, Up To 32 CPU Lic, 3 YR Sub, DIB, Media [$699.00]. > > Also, although might be a stupid question, I am supposed to transfer files from the server to a pc back and forth. I am not sure whether I will need software to change files written on a pc with the notepad windows operating system and those written Linux operating system. > > Best regards, > Adel El-Azhary> > > From owner-chemistry@ccl.net Wed Jun 23 00:35:00 2010 From: "John McKelvey jmmckel(_)gmail.com" To: CCL Subject: CCL: Linux operating system Message-Id: <-42150-100622232620-2127-slb1eHxcP5Gleo4bsz58YA===server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 22 Jun 2010 23:26:13 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel[]gmail.com] You might consider CENTOS 5.3 or 5.4.... a non commercial, free version of RH 5.3 also John McKelvey On Tue, Jun 22, 2010 at 7:10 PM, Adel El-Azhary azhary+/-ksu.edu.sa wrote: > > Sent to CCL by: "Adel  El-Azhary" [azhary.:.ksu.edu.sa] > Dear CCL members. > > We are planning to buy a dell power server with two Xeon processors. There are three options of the operating system. Does anyone have a preference for any of them, other than the price? The three operating systems are: > > 1. Red Hat Enterprise Linux 5.3, 2S, FI x64, 3yr, Auto-Entitle, Lic & Media [$1,099.00]. > 2. SUSE Linux Enterprise Server 11, 1-2CPU, 3 YR Subscription, FI, Media [$349.00]. > 3. SUSE Linux Enterprise Server 10, SP3, Up To 32 CPU Lic, 3 YR Sub, DIB, Media [$699.00]. > > Also, although might be a stupid question, I am supposed to transfer files from the server to a pc back and forth. I am not sure whether I will need software to change files written on a pc with the notepad windows operating system and those written Linux operating system. > > Best regards, > Adel El-Azhary>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel]![gmail.com From owner-chemistry@ccl.net Wed Jun 23 04:20:00 2010 From: "Gang Feng fegg7502.%x%.gmail.com" To: CCL Subject: CCL: How many International conferences on CC in 2011-2015? Message-Id: <-42151-100623041800-23710-53+o1hVeJM2XQqPXhbeUug%x%server.ccl.net> X-Original-From: "Gang Feng" Date: Wed, 23 Jun 2010 04:17:59 -0400 Sent to CCL by: "Gang Feng" [fegg7502[A]gmail.com] Dear All: Could anyone give me some information on the international conferences on Computational Chemistry in the coming 2011-2015 years? Thank you very much in advance! Best regards! Yours sincerely! Gang From owner-chemistry@ccl.net Wed Jun 23 07:29:01 2010 From: "Jo o Henriques joao.henriques.32353|*|gmail.com" To: CCL Subject: CCL: Gaussian03 frequency calculation error Message-Id: <-42152-100623070101-2924-2BZu1+asIyv/G9iU9IfMUQ|*|server.ccl.net> X-Original-From: "Jo o Henriques" Date: Wed, 23 Jun 2010 07:01:00 -0400 Sent to CCL by: "Jo o Henriques" [joao.henriques.32353^_^gmail.com] Dear All, I am doing some frequency calculations over optimized heme models. The system is paramagnetic and here are the flags used in the calculation: ----------------------------------------------------------------------------- - %NProcShared=1 %Mem=1Gb %Chk=xxx.chk %rwf=1,245mw,2,245mw,3,245mw,4,245mw,5,245mw,6,245mw,7,245mw,8,245mw,9,245mw, 10,245mw,11,245mw,12,245mw,13,245mw,14,245mw,15,245mw,16,245mw # B3LYP/Gen Pseudo=Read Guess=Read Geom=Checkpoint Freq SCF=Tight xxx 1 2 ----------------------------------------------------------------------------- - I'm using 6-31G(2df) for H O N C S and LANL2TZ(f) for Fe. Radius of 1.5 for Fe. I use the checkpoint from the opt calculations as an initial guess. However I get this error roughly after a week of calculation: ---------------------------- Error termination in NtrErr: NtrErr called from FIOCnC. ---------------------------- All the forums I checked weren't very helpful, so I still have no idea of what's going on. The analog diamagnetic calculations terminate normally. The .rwf files are sufficient, with only up to 10 of them being written. Therefore I would appreciate any input on what you might think that is happening and what kind of error is this. From what I've seen it doesn't seem to be a very common one. Thank in advance, Best regards, Joo Henriques From owner-chemistry@ccl.net Wed Jun 23 11:11:00 2010 From: "Vincent Leroux vincent.leroux#%#loria.fr" To: CCL Subject: CCL: Linux operating system Message-Id: <-42153-100623050200-5764-43h8eXmuNQNdqi/yCtRj2g*server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 23 Jun 2010 11:01:49 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux*o*loria.fr] Hello, I would strongly recommend Scientific Linux as a RHEL variant like CENTOS is. The level of support is particularly good, and the distribution suits clusters as well as workstations. https://www.scientificlinux.org/ Regards VL Le 23/06/10 05:26, John McKelvey jmmckel(_)gmail.com a écrit : > > Sent to CCL by: John McKelvey [jmmckel[]gmail.com] > You might consider CENTOS 5.3 or 5.4.... a non commercial, free > version of RH 5.3 also > > John McKelvey > > On Tue, Jun 22, 2010 at 7:10 PM, Adel El-Azhary azhary+/-ksu.edu.sa > wrote: >> >> Sent to CCL by: "Adel El-Azhary" [azhary.:.ksu.edu.sa] >> Dear CCL members. >> >> We are planning to buy a dell power server with two Xeon processors. There are three options of the operating system. Does anyone have a preference for any of them, other than the price? The three operating systems are: >> >> 1. Red Hat Enterprise Linux 5.3, 2S, FI x64, 3yr, Auto-Entitle, Lic & Media [$1,099.00]. >> 2. SUSE Linux Enterprise Server 11, 1-2CPU, 3 YR Subscription, FI, Media [$349.00]. >> 3. SUSE Linux Enterprise Server 10, SP3, Up To 32 CPU Lic, 3 YR Sub, DIB, Media [$699.00]. >> >> Also, although might be a stupid question, I am supposed to transfer files from the server to a pc back and forth. I am not sure whether I will need software to change files written on a pc with the notepad windows operating system and those written Linux operating system. >> >> Best regards, >> Adel El-Azhary> >> >> > > > From owner-chemistry@ccl.net Wed Jun 23 11:46:00 2010 From: "Close, David M. CLOSED||mail.etsu.edu" To: CCL Subject: CCL:G: problem with imaginery frequency and keyword modredundant in G03 Message-Id: <-42154-100622144324-13843-WX+Gj2xr7YtQDCsHIKW0fQ::server.ccl.net> X-Original-From: "Close, David M." Content-Class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CB123A.AB0FA3DA" Date: Tue, 22 Jun 2010 14:42:29 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED---mail.etsu.edu] ------_=_NextPart_001_01CB123A.AB0FA3DA Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Valya: You have to be more specific. What is the frequency? If it is real = small this may just be an artifact. It could for example be associated = with an unimportant rotation (say of a methyl group?) If however this = is a normal vibration, you have converged to a transition state. You = have to animate the vibration to see if the frequency corresponds to = motion along the reaction path. If so, you can displace the molecule = along the direction of the vibration, and the optimization routine = should converge to a proper optmized geometry. Regards, Dave Close ________________________________ > From: owner-chemistry+closed=3D=3Detsu.edu|a|ccl.net on behalf of Valya = Nikolova ohtvd..chem.uni-sofia.bg Sent: Tue 6/22/2010 10:36 AM To: Close, David M. Subject: CCL: problem with imaginery frequency and keyword modredundant = in G03 Sent to CCL by: "Valya Nikolova" [ohtvd:chem.uni-sofia.bg] hello, I will be very appreciate, if someone can help me. I done hydrogen = bonded complexes with option modredundant, and I have 1 imaginery = frequency in the out file. How can I remove it, and is it exists every = time when you work with modredundant. thanck you in advance -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml= =20http://www.ccl.net/spammers.txt------_=_NextPart_001_01CB123A.AB0FA3DA-- From owner-chemistry@ccl.net Wed Jun 23 12:20:00 2010 From: "Tim Cheeseright tim.:.cresset-bmd.com" To: CCL Subject: CCL: FieldView - free molecular viewer / editor just released Message-Id: <-42155-100623120944-13844-NDaxASCS/q4W9rW4NM6U1Q-#-server.ccl.net> X-Original-From: "Tim Cheeseright" Date: Wed, 23 Jun 2010 12:09:43 -0400 Sent to CCL by: "Tim Cheeseright" [tim]![cresset-bmd.com] Cresset are excited to announce the release and free download of FieldView (from http://www.cresset-group.com/product/fieldview), a powerful new Chemistry tool, providing insights into the properties and activities of your molecules. Instead of relying on 2D structure, Cresset uses the Fields around molecules to assess their likely activity and properties, regardless of structural similarity. Find out more at www.cresset-group.com/page/technology You can use FieldView to: * Understand how a compound's activity, ADME and toxicity properties vary with their molecular Fields. * Automatically convert structures from 2D to a minimized 3D conformation * View virtual screening results, such as those from FieldScreen, comparing 2D structures with 3D overlay showing all the Fields of every ligand. * Create new structures using the in-built molecular editor, or clone and modify existing compounds to create a series of analogues. * Compare compounds side by side or overlaid using Cresset's unique Field technology to better understand their activity and properties * Filter molecules based on the exact mix of properties you need. Unsupported single user licenses for FieldView are available for free at http://www.cresset-group.com/product/fieldview Fully supported site and global licenses are also available, contact george!=!cresset-group.com Tim Cheeseright (tim!=!cresset-group.com) Cresset UK From owner-chemistry@ccl.net Wed Jun 23 14:17:00 2010 From: "=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes jafernandes|*|ua.pt" To: CCL Subject: CCL: Gaussian03 frequency calculation error Message-Id: <-42156-100623140927-8649-3Mhg4NOI6BRG68W6N8CBmg=-=server.ccl.net> X-Original-From: "=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1;format="flowed" Date: Wed, 23 Jun 2010 19:08:53 +0100 MIME-Version: 1.0 Sent to CCL by: "=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes" [jafernandes/a\ua.pt] Hello Can you use more memory? 1 Gb seems to be to short for frequency calculations. I've been trying to calculate frequencies for big systems and errors like these appear some days after the process starts. The diamagnetic process works because it needs shorter memory. Em Wed, 23 Jun 2010 07:01:00 -0400 "Jo o Henriques joao.henriques.32353|*|gmail.com" escreveu: > > Sent to CCL by: "Jo o Henriques" >[joao.henriques.32353^_^gmail.com] > Dear All, > > I am doing some frequency calculations over optimized >heme models. The system > is paramagnetic and here are the flags used in the >calculation: > > ----------------------------------------------------------------------------- > - > %NProcShared=1 > %Mem=1Gb > %Chk=xxx.chk > %rwf=1,245mw,2,245mw,3,245mw,4,245mw,5,245mw,6,245mw,7,245mw,8,245mw,9,245mw, > 10,245mw,11,245mw,12,245mw,13,245mw,14,245mw,15,245mw,16,245mw > # B3LYP/Gen Pseudo=Read Guess=Read Geom=Checkpoint Freq >SCF=Tight > > xxx > > 1 2 > > ----------------------------------------------------------------------------- > - > > I'm using 6-31G(2df) for H O N C S and LANL2TZ(f) for >Fe. > Radius of 1.5 for Fe. > I use the checkpoint from the opt calculations as an >initial guess. > > However I get this error roughly after a week of >calculation: > > ---------------------------- > Error termination in NtrErr: > NtrErr called from FIOCnC. > ---------------------------- > > All the forums I checked weren't very helpful, so I >still have no idea of > what's going on. > The analog diamagnetic calculations terminate normally. >The .rwf files are sufficient, with only up to 10 of them >being written. > > Therefore I would appreciate any input on what you might >think that is > happening and what kind of error is this. From what I've >seen it doesn't seem > to be a very common one. > > Thank in advance, > Best regards, > > Joo Henriques > > > > -= This is automatically added to each message by the >mailing script =- > To recover the email address of the author of the >message, please change > the strange characters on the top line to the = sign. >You can also> > E-mail to administrators: CHEMISTRY-REQUEST=ccl.net or >use> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: >http://www.ccl.net/chemistry/searchccl/index.shtml> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/ > > José Fernandes Departamento de Quimica Universidade de Aveiro 3810-193 Aveiro Portugal Tel: +351234370720 Fax: +351234370084 From owner-chemistry@ccl.net Wed Jun 23 15:30:01 2010 From: "Kurt De Grave Kurt.DeGrave _ cs.kuleuven.be" To: CCL Subject: CCL: Linux operating system Message-Id: <-42157-100623073551-12544-2t+iDqin8OgH0ZX0HMBKAQ|,|server.ccl.net> X-Original-From: Kurt De Grave Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 23 Jun 2010 13:35:30 +0200 MIME-Version: 1.0 Sent to CCL by: Kurt De Grave [Kurt.DeGrave++cs.kuleuven.be] Jason Swails jason.swails() gmail.com wrote: > If it's at all a consideration, I'd choose SUSE 11. If the > 2 Xeon processors are multi-core, which I expect they are, I'd choose SUSE > 10 (since it's licensed up to 32 CPUs). If you plan to get multiple servers > and cluster them (more than 32 CPUs), I'd do Red Hat for sure. In this context, CPUs most probably means sockets, not cores. I'd be quite hard to find a 1-2 core server today :-). The SLES 11 limit should be fine for a two-socket server. The 2 socket limit is just price discrimination AFAIK. Almost all OS vendors do that. If the customer can afford a $50,000+, 4+ socket server, he can probably afford to pay a little extra for the OS as well. Technically, SLES 11 supports 4096 CPU cores. Note that these prices probably include just 3YR online patches and some short-lived burn-in support, not 3YR support by human experts. With free Linux versions you have to look out for two issues: some of them have only a very limited period of security patches per release, and you don't want to be forced to upgrade your server OS every year. Also, if the server hardware is exotic and/or very new, it might not be fully supported by the free distro, potentially creating severe headaches, especially if you're a novice Linux admin. Not all Linux developers have your particular RAID card model or server chipset. If the OEM guarantees that a given distro will work with that particular hardware, that's worth something. It all depends on how much you value availability of the system and your time to install and maintain it. There are free distro's with long support life cycles: e.g. the LTS version of Ubuntu, some Red Hat clones, or Debian stable. The excellent openSUSE distro used to be supported for two years which was just enough for a number of use cases, but unfortunately they've throttled it back to about 18 months, I assume at least partially to reduce cannibalism of SLES. If a long-term supported free distro happens to work well, you're settled. If the application is important enough and you don't want to take the risk, go for SLES 11. Here, in this CS department, we run unsupported (i.e. internally supported) (K)Ubuntu on most systems, with maybe a few relic Debian or Solaris instances left. We've got several capable admins and they tend to avoid exotic hardware. best regards, kurt. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Wed Jun 23 18:31:01 2010 From: "Claudia ------------- Escobar iqclaudia_428^_^hotmail.com" To: CCL Subject: CCL: GROMACS PROGRAM Message-Id: <-42158-100623104706-17326-1RGkR3x6ksLnpwb8SS7pxA|-|server.ccl.net> X-Original-From: "Claudia ------------- Escobar" Date: Wed, 23 Jun 2010 10:47:05 -0400 Sent to CCL by: "Claudia ------------- Escobar" [iqclaudia_428/./hotmail.com] Dear all: I'm trying to make a run on GROMACS (molecular dynamics) but the system I have is an aldehyde with alcohol. This program comes with tutorials only protein and water as a solvent. Someone could help me. Thank you very much Claudia Escobar UTN-FRRE