From owner-chemistry@ccl.net Tue Jun 22 12:43:01 2010 From: "Valya Nikolova ohtvd..chem.uni-sofia.bg" To: CCL Subject: CCL: problem with imaginery frequency and keyword modredundant in G03 Message-Id: <-42142-100622103604-30380-9/BO6zVaZTSJV6IXPsFC1g/./server.ccl.net> X-Original-From: "Valya Nikolova" Date: Tue, 22 Jun 2010 10:36:03 -0400 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 From owner-chemistry@ccl.net Tue Jun 22 18:01:00 2010 From: "Ol Ga eurisco1|a|pochta.ru" To: CCL Subject: CCL:G: problem with imaginery frequency and keyword modredundant in G03 Message-Id: <-42143-100622141559-26689-kdWw+u8xlPskR7i+9T8E0g##server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 22 Jun 2010 14:15:58 -0400 Sent to CCL by: "Ol Ga" [eurisco1||pochta.ru] Dear Valya Nikolova, If the structure is not FULLY optimized, you can observe imaginary frequency or frequencies as well as it is possible that non-optimized structure has not any imaginary frequency. To remove imaginary frequency you should perform geometry opt without constraints. It is better to think why do you need modredundant option. Possible you can just ignore imag freq. It depends strongly on your aim or subject of your research etc. Sincerely, Ol Ga > From: "Valya Nikolova ohtvd..chem.uni-sofia.bg" > Sent: Tuesday, June 22, 2010 6:36 PM > To: "Ga, Ol " > 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 From owner-chemistry@ccl.net Tue Jun 22 18:36:00 2010 From: "Olexandr Isayev olexandr.isayev{=}case.edu" To: CCL Subject: CCL: 19th Conference on Current Trends in Computational Chemistry (October 29-30, 2010) Message-Id: <-42144-100622140034-23047-CXsmfGHwDXDZlOVBfyXXXg]![server.ccl.net> X-Original-From: Olexandr Isayev Content-Type: multipart/alternative; boundary=000e0cdf1a300d4c060489a23203 Date: Tue, 22 Jun 2010 13:00:04 -0500 MIME-Version: 1.0 Sent to CCL by: Olexandr Isayev [olexandr.isayev:_:case.edu] --000e0cdf1a300d4c060489a23203 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable ** With apologies for cross-posting ** http://cctcc.icnanotox.org 19th Conference on Current Trends in Computational Chemistry (October 29-30, 2010) We are pleased to announce and to invite you to attend the 19th Conference on Current Trends in Computational Chemistry (CCTCC) on October 30-31, 2009= . This symposium, organized by Jackson State University, covers all areas of computational and quantum chemistry. The format consists of a series of (invited) plenary lectures and poster presentations on Friday and Saturday covering applications as well as theory. Registration and abstract submission is open until September 1, 2010. Venue: As usual the conference will be held at the Hilton Jackson Hotel, Jackson, Miss. (USA). Tentative list of invited speakers: Vlasta Bonacic-Koutecky, *Humbolt University Berlin, Germany* Benoit R. Champagne, *Universit=E9 Notre Dam de la Paix, Belgium* James R. Chelikowsky, *University of Texas* Slawomir J. Grabowski, *Euskal Herriko Unibertsitatea, Spain* Robert J. Harrison, *Oak Ridge National Laboratory* Martin Head-Gordon, *University of California Berkeley* Bern Kohler, *Montana State University* Marc C. Nicklaus, *National Cancer Institute* Jozef Noga, *Comenius University, Slovakia* Karlheintz Schwarz, *Technische Universitat Wien, Austria* Sakaki Shigeyoshi, *University of Kyoto, Japan* Sergei Tretiak,* Los Alamos National Laboratory* Donald Truhlar, *University of Minnesota* Angela K. Wilson, *University of North Texas* All details about registration, abstracts and housing may be found at http://cctcc.icnanotox.org Questions? Email us at cctcc!=!icnanotox.org Please also feel free to forward this invitation to other potentially interested colleagues. We look forward to seeing you in Jackson this Fall! On behalf of the Organizing Committee, Olexandr Isayev ________________________________ Olexandr Isayev, Ph.D. Department of Chemistry Case Western Reserve University 10900 Euclid Avenue Cleveland, OH 44106-7078 USA Phone: 769 218-9812 Fax: 216 368-3006 http://olexandrisayev.com --000e0cdf1a300d4c060489a23203 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable ** With apologies for cross-posting **

http://cctcc.icnanotox.org

19th Conference on Current Trends in Computational Chemistry
(October= =20 29-30, 2010)

We are pleased to announce and to invite you to attend the 19th=20 Conference on Current Trends in Computational Chemistry (CCTCC) on October = 30-31, 2009. This symposium, organized by Jackson State=20 University, covers all areas of computational and quantum chemistry. The format consists of a series of (invited) plenary lectures and poster=20 presentations on Friday and Saturday covering applications as well as=20 theory.

Registration and abstract submission is open until September 1, 2010.

Venue:
As usual the conference will be held at the Hilton Jackson Hotel,=20 Jackson, Miss. (USA).

Tentative list of invited speakers:
Vlasta Bonacic-Koutecky, Humbolt University Berlin, Germany
Benoit R. Champagne, Universit=E9 Notre Dam de la Paix, Belgium
James R. Chelikowsky, University of Texas
Slawomir J. Grabowski, Euskal Herriko Unibertsitatea, Spain
Robert J. Harrison, Oak Ridge National Laboratory
Martin Head-Gordon, University of California Berkeley
Bern Kohler, Montana State University
Marc C. Nicklaus, National Cancer Institute
Jozef Noga, Comenius University, Slovakia
Karlheintz Schwarz, Technische Universitat Wien, Austria
Sakaki Shigeyoshi, University of Kyoto, Japan
Sergei Tretiak, Los Alamos National Laboratory
Donald Truhlar, University of Minnesota
Angela K. Wilson, University of North Texas

All details about registration, abstracts and housing may be found at http://cctcc.icnanotox.org

Questions? Email us at cctcc!=!icnanot= ox.org

Please also feel free to forward this invitation to other potentially=20 interested colleagues.

We look forward to seeing you in Jackson this Fall!

On behalf of the Organizing Committee,
Olexandr Isayev


________________________________<= br>Olexandr Isayev, Ph.D.

Department of Chemistry
Case Western Reserve University
10900 Euclid Avenue
Cleveland, OH 44106-7078 USA

Phone:=A0 769=20 218-9812
Fax: =A0 =A0 =A0 216 368-3006

http://olexandrisayev.com

--000e0cdf1a300d4c060489a23203-- From owner-chemistry@ccl.net Tue Jun 22 20:31:00 2010 From: "Adel El-Azhary azhary+/-ksu.edu.sa" To: CCL Subject: CCL: Linux operating system Message-Id: <-42145-100622191036-9234-l83xR0quMRdR1i/T7VXnyQ]^[server.ccl.net> X-Original-From: "Adel El-Azhary" Date: Tue, 22 Jun 2010 19:10:33 -0400 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 Tue Jun 22 22:16:00 2010 From: "Jan Labanowski janl.:.speakeasy.net" To: CCL Subject: CCL: Linux operating system Message-Id: <-42146-100622221015-3007-CIuap1p4+2HjH+sF2M3uKA###server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Tue, 22 Jun 2010 22:10:08 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl###speakeasy.net] Adel El-Azhary writes: > 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]. In my opinion RHEL makes only sense if you need security and reliability (e.g., you would do bank transactions or personnel files) or if you wanted to use some graphics cards that are only supported under RHEL due to commecial, closed source XFree drivers (e.g., higher end ATI cards). But since this computer is for number crunching, you do not even want to run X-window on it and you will be accessing it from Windoz using Cygwin (UNIX subsystem that runs under Windoz and is free: http://www.cygwin.com) using ssh (the server like this is noisy and quite hot, and you do not want to keep it under your desk). Spent money on more memory. For a research system I would just use Fedora 13. Suse is less expensive and quite reliable. However, it is less popular in USA, so if you want to install RPMs of some less popular packages, you may have some problems. But you can always recompile open source and you should not have any problems with SUSE since it is very similar to Fedora/RedHat layout. Now, with the "pre-upgrade" option, it is easy to upgrade to the next release of Fedora when it goes out of active support. While Ubuntu/Debian are solid systems and easy to maintain, I would not touch them since compiling and developing software on them is a pain, unless you have long experience with them, since these guys "know better" (maybe for a good reason, but you want to go with the crowd... It is easier.) The Ubuntu/Debian folks made layout and administration quite different than on other popular Linuces. Some people love it, I hate it... Converting Notpad files (with LineBreaks ^M^J) to Linux files (LineBreaks ^J) is easy: dos2unix -o UnixFile -n DosFile check man page for dos2unix. I personally just use emacs and replace the ^M with an empty string. Jan From owner-chemistry@ccl.net Tue Jun 22 22:51:00 2010 From: "Jason Rigby Jason.Rigby[a]monash.edu" To: CCL Subject: CCL: Linux operating system Message-Id: <-42147-100622214523-3188-Eukia90UMSS9johhVk2CcA:-:server.ccl.net> X-Original-From: Jason Rigby Content-Type: multipart/alternative; boundary=00151750e14c6b1b4e0489a8b05a Date: Wed, 23 Jun 2010 11:44:54 +1000 MIME-Version: 1.0 Sent to CCL by: Jason Rigby [Jason.Rigby*|*monash.edu] --00151750e14c6b1b4e0489a8b05a Content-Type: text/plain; charset=ISO-8859-1 Dear Adel, I don't have a particular preference towards the operating systems, but as for transferring files, it really depends on how the files were created in the first place and what the file format is (ASCII text, for example). Unix operating systems handle new-line characters differently, so a text file generated in a Unix-based operating system may appear broken when opened in Windows. There are commands in linux such as 'unix2dos' or 'dos2unix' which will fix this, but these days I find that it is as simple as opening the file in a lightly more sophisticated text editor than Notepad (such as WordPad) in order to view them correctly. I hope this at least addresses part of your question! Kind regards, Jason On 23 June 2010 09:10, Adel El-Azhary azhary+/-ksu.edu.sa < owner-chemistry,ccl.net> 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> > > --00151750e14c6b1b4e0489a8b05a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Adel,
I don't have a particular preference towards the operati= ng systems, but as for transferring files, it really depends on how the fil= es were created in the first place and what the file format is (ASCII text,= for example). Unix operating systems handle new-line characters differentl= y, so a text file generated in a Unix-based operating system may appear bro= ken when opened in Windows. There are commands in linux such as 'unix2d= os' or 'dos2unix' which will fix this, but these days I find th= at it is as simple as opening the file in a lightly more sophisticated text= editor than Notepad (such as WordPad) in order to view them correctly.
I hope this at least addresses part of your question!

Kind regards,
Jason

On= 23 June 2010 09:10, Adel El-Azhary azhary+/-= ksu.edu.sa <owner-chemistry,ccl.net> wrote:

Sent to CCL by: "Adel =A0El-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 fo= r 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 & M= edia [$1,099.00].
2. SUSE Linux Enterprise Server 11, 1-2CPU, 3 YR Subscription, FI, Media [$= 349.00].
3. SUSE Linux Enterprise Server 10, SP3, Up To 32 CPU Lic, 3 YR Sub, DIB, M= edia [$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 s= oftware to change files written on a pc with the notepad windows operating = system and those written Linux operating system.

Best regards,
Adel El-Azhary



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--00151750e14c6b1b4e0489a8b05a-- From owner-chemistry@ccl.net Tue Jun 22 23:26:00 2010 From: "Jason Swails jason.swails() gmail.com" To: CCL Subject: CCL: Linux operating system Message-Id: <-42148-100622220743-28827-uBzmZ/PfiyWeJUxBjZFh3w%server.ccl.net> X-Original-From: Jason Swails Content-Type: multipart/alternative; boundary=0016e6480dba3537750489a9009e Date: Tue, 22 Jun 2010 22:07:32 -0400 MIME-Version: 1.0 Sent to CCL by: Jason Swails [jason.swails*gmail.com] --0016e6480dba3537750489a9009e Content-Type: text/plain; charset=ISO-8859-1 Hello, Our clusters all run CentOS, which is the open source portion of Red Hat. You can download and install CentOS for free, and you have Red Hat without the professional support (installation is easy -- just follow the on-screen prompts). You can also download openSUSE which is the same as SUSE Linux Enterprise without the professional support. If there's someone on hand that's reasonably Linux/unix-savvy, I would probably opt for one of the open-source versions of the below rather than the paid ones. Otherwise, look at the difference in the licenses. 2 and 3 (SUSE) are limited in how many CPUs they can run on. In terms of usability, features, and performance, they both run the same kernel, so you probably won't notice much of a difference between them. I've given you the standard response on most computer forums, which is "none of your options are good, you really want to consider my option," which tends to drive me nuts. So here's my direct answer to your question, assuming you're set in your reasons for going with the enterprise version (of course, it's only my opinion): if money is no object whatsoever, I'd choose Red Hat. 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. Both linux-es should come with dos2unix and unix2dos, which should convert text files created by notepad/Windows to/from unix format (which differ in their newline characters, or something of the like). Other than that, file conversions are necessary on a program-by-program basis (i.e. openoffice can read/write microsoft office formats). It was a long-winded response, but I hope it helps, Jason On Tue, Jun 22, 2010 at 7:10 PM, Adel El-Azhary azhary+/-ksu.edu.sa < owner-chemistry~!~ccl.net> 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> > > -- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 --0016e6480dba3537750489a9009e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,

Our clusters all run CentOS, which is the open source portion= of Red Hat.=A0 You can download and install CentOS for free, and you have = Red Hat without the professional support (installation is easy -- just foll= ow the on-screen prompts).

You can also download openSUSE which is the same as SUSE Linux Enterpri= se without the professional support.=A0 If there's someone on hand that= 's reasonably Linux/unix-savvy, I would probably opt for one of the ope= n-source versions of the below rather than the paid ones.=A0 Otherwise, loo= k at the difference in the licenses.=A0 2 and 3 (SUSE) are limited in how m= any CPUs they can run on.=A0 In terms of usability, features, and performan= ce, they both run the same kernel, so you probably won't notice much of= a difference between them.

I've given you the standard response on most computer forums, which= is "none of your options are good, you really want to consider my opt= ion," which tends to drive me nuts.=A0 So here's my direct answer = to your question, assuming you're set in your reasons for going with th= e enterprise version (of course, it's only my opinion): if money is no = object whatsoever, I'd choose Red Hat.=A0 If it's at all a consider= ation, I'd choose SUSE 11.=A0 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).=A0 If you plan to get multiple servers and cluster them (more= than 32 CPUs), I'd do Red Hat for sure.

Both linux-es should come with dos2unix and unix2dos, which should conv= ert text files created by notepad/Windows to/from unix format (which differ= in their newline characters, or something of the like).=A0 Other than that= , file conversions are necessary on a program-by-program basis (i.e. openof= fice can read/write microsoft office formats).

It was a long-winded response, but I hope it helps,

Jason
On Tue, Jun 22, 2010 at 7:10 PM, Adel El-Azhary= azhary+/-ksu.edu.sa &l= t;owner-chemistry~!~ccl.net>= ; wrote:

Sent to CCL by: "Adel =A0El-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 fo= r 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 & M= edia [$1,099.00].
2. SUSE Linux Enterprise Server 11, 1-2CPU, 3 YR Subscription, FI, Media [$= 349.00].
3. SUSE Linux Enterprise Server 10, SP3, Up To 32 CPU Lic, 3 YR Sub, DIB, M= edia [$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 s= oftware to change files written on a pc with the notepad windows operating = system and those written Linux operating system.

Best regards,
Adel El-Azhary



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Jason M. Swails
Quan= tum Theory Project,
University of Florida
Ph.D. Graduate Student
3= 52-392-4032
--0016e6480dba3537750489a9009e--