From owner-chemistry@ccl.net Tue Feb 12 10:24:01 2008 From: "David Gallagher gallagher.da^-^gmail.com" To: CCL Subject: CCL: Properties of mixtures? Message-Id: <-36268-080211225052-4864-xQ7EbTtdeIdi7SQo6OFY8w*server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_42432578==.ALT" Date: Mon, 11 Feb 2008 18:55:26 -0800 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da**gmail.com] --=====================_42432578==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Predicting properties of mixtures? Properties of mixtures such as drug formulations, personal care products, fragrances, dyes, inks, additives, ionic liquids, distillations, reactions, etc. can now be predicted more accurately with the latest release of COSMOtherm. COSMOtherm version C2.1 release 01.07 This new release includes improved parameters (BP-TZVP-COSMO) and an enhanced fitting procedure validated on a massively enlarged set of experimental data, improving prediction of properties such as solubilities, partition coefficients, LogP, activity coefficients, VLE data, etc. at a wide range of temperatures. Additional improvements have been obtained by taking into account conformations and the free energy of fusion for solids. For further information or release notes, visit: http://www.cacheresearch.com/cosmo.html The award-winning COSMOtherm is based on the published COSMO-RS methodology, a unique blend of DFT and statistical thermodynamics. It makes a priori property predictions on mixtures and pure compounds, and runs on Windows and Linux platforms. The new release is available free > from COSMOlogic for users with a current support contract. David Gallagher CACheResearch.com --=====================_42432578==.ALT Content-Type: text/html; charset="us-ascii" Predicting properties of mixtures?
Properties of mixtures such as drug formulations, personal care products,
fragrances, dyes, inks, additives, ionic liquids, distillations, reactions, etc.
can now be predicted more accurately with the latest release of COSMOtherm.

COSMOtherm version C2.1 release 01.07
This new release includes improved parameters (BP-TZVP-COSMO) and an
enhanced fitting procedure validated on a massively enlarged set of
experimental data, improving prediction of properties such as solubilities,
partition coefficients, LogP, activity coefficients, VLE data, etc. at a wide
range of temperatures.  Additional improvements have been obtained by
taking into account conformations and the free energy of fusion for solids.

For further information or release notes, visit:
     http://www.cacheresearch.com/cosmo.html

The award-winning COSMOtherm is based on the published COSMO-RS
methodology, a unique blend of DFT and statistical thermodynamics.  It
makes a priori property predictions on mixtures and pure compounds, and
runs on Windows and Linux platforms.  The new release is available free
> from COSMOlogic for users with a current support contract.

David Gallagher
CACheResearch.com
--=====================_42432578==.ALT-- From owner-chemistry@ccl.net Tue Feb 12 11:03:00 2008 From: "John McKelvey jmmckel|gmail.com" To: CCL Subject: CCL: Disk striping Message-Id: <-36269-080212105147-2751-JzBuRS5Ru5KE5tbV9MHSfQ:_:server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_48756_18036285.1202831047497" Date: Tue, 12 Feb 2008 10:44:07 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel..gmail.com] ------=_Part_48756_18036285.1202831047497 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello! On a dual-dual RHEL4 machine I am doing some MP2 calculations that have a serious IO overhead issues when other jobs need some IO. I would like to add a software Raid 0 [after adding two identical Seagate 7200.10 or 7200.11drives] to this machine... if I knew how. Could someone point me to some info on how to do this? Many thanks! John McKelvey ------=_Part_48756_18036285.1202831047497 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello!

On a dual-dual RHEL4 machine I am doing some MP2 calculations  that have a serious IO overhead issues when other jobs need some IO.  I would like to add a software Raid 0 [after adding two identical Seagate 7200.10 or 7200.11 drives] to this machine... if I knew how.  Could someone point me to some info on how to do this?

Many thanks!

John McKelvey
------=_Part_48756_18036285.1202831047497-- From owner-chemistry@ccl.net Tue Feb 12 12:58:01 2008 From: "Herbert Fruchtl herbert.fruchtl-,-st-andrews.ac.uk" To: CCL Subject: CCL: Disk striping Message-Id: <-36270-080212125039-27425-m/tnUWX/mB+LPLbghNs37g]-[server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 12 Feb 2008 17:50:05 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl ~ st-andrews.ac.uk] Hi John, I did that once a few years ago, following the instructions in the following HOWTO: http://tldp.org/HOWTO/Software-RAID-HOWTO.html This might be a bit out of date by now (it's about kernel 2.4), but should still work. I haven't tried the following, but it looks sufficiently detailed (and mentions that you might just do it automatically by installing Linux from scratch): http://www.enterprisestorageforum.com/technology/features/article.php/3526891 Cheers, Herbert John McKelvey jmmckel|gmail.com wrote: > Hello! > > On a dual-dual RHEL4 machine I am doing some MP2 calculations that have > a serious IO overhead issues when other jobs need some IO. I would like > to add a software Raid 0 [after adding two identical Seagate 7200.10 or > 7200.11 drives] to this machine... if I knew how. Could someone point > me to some info on how to do this? > > Many thanks! > > John McKelvey -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Tue Feb 12 13:33:00 2008 From: "Aleksey Kuznetsov AlexKuznetsov2007++yandex.ru" To: CCL Subject: CCL:G: Problem with Gaussian frequency calculation - "OrtVc1 failed #1" message Message-Id: <-36271-080212122033-25640-QFVkWDEHn2hdPvFzobcALA!^!server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 12 Feb 2008 19:44:04 +0300 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007/./yandex.ru] Dear CCL Subscribers, I'd like to ask you for a piece of advice on the following problem: I try to perform frequency calculations (using Gaussian) for polyoxometalate (POM) systems containing 58 atoms (C1 symmetry), at the B3LYP/LanL1DZ level (601 basis functions), with memory set to 150MW and MAXDISK set to 950000000; these calculations crash at certain point producing the following output (these are just several ending lines of the output file): " There are 177 degrees of freedom in the 1st order CPHF. 177 vectors were produced by pass 0. AX will form 59 AO Fock derivatives at one time. 177 vectors were produced by pass 1. OrtVc1: IOff= 0 IPass= 5 DotMx1= 4.98D-08 OrtVc1: M= 163480 NPass= 5 Test1= 9.24D-14 Small= 1.63D-08 VSmall= 1.00D-12 OrtVc1 failed #1. Error termination via Lnk1e in /usr/local/lib2/GDVD01+/gdv/l1002.exe at Mon Feb 11 05:17:26 2008. Job cpu time: 1 days 8 hours 8 minutes 40.5 seconds. File lengths (MBytes): RWF= 3866 Int= 0 D2E= 0 Chk= 43 Scr= 1 " However, at the B3LYP/LanL2mb level such calculations run without any problems. Could anybody advise me about the reason of the above issue? Is it the memory and disk space problem, or is anything else involved? Thank you very much in advance. With best regards, Aleksey Kuznetsov. ------------------------------------------- Dr. Aleksey Kuznetsov Cherry L. Emerson Center for Scientific Computation Emory University 1515 Dickey Drive Atlanta, GA 30322 USA Phone: (404)727-2381 Email: akuznets\a/euch4e.chem.emory.edu ------------------------------------------- From owner-chemistry@ccl.net Tue Feb 12 14:08:00 2008 From: "Jozsef Csontos jozsefcsontos ~~ creighton.edu" To: CCL Subject: CCL: Disk striping Message-Id: <-36272-080212132204-6213-+CKpVwiNIjsab6VZTGo7pA%x%server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 12 Feb 2008 12:21:52 -0600 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos_+_creighton.edu] Hi, you can find the raid-howto (section raid0)here: http://unthought.net/Software-RAID.HOWTO/Software-RAID.HOWTO-5.html#ss5.5 Basically, after you installed the hardware the following steps are needed: (Let's suppose your newly installed disks are /dev/sdc and /dev/sdd) a, su -l b, setup new software raid partitions with fdisk ("fdisk /dev/sdc" and "fdisk /dev/sdd"; new partition (n) -> primary (p) -> partition number (1) -> default size (enter, enter) -> change type (t) -> Linux raid autodetect (fd) -> print the info (p) -> if everything is fine then write the partition table and quit (w). c, create the raid with mdadm (this program should be available under redhat); "mdadm --create /dev/md0 --level=0 --raid-devices=2 /dev/sdc1 /dev/sdd1" d, you should also put a line into the /etc/fstab file (/dev/md0 your_mount_point ...) You can check the status of the raid: "cat /proc/mdstat" I hope it helps, Jozsef On Tue, 2008-02-12 at 10:44 -0500, John McKelvey jmmckel|gmail.com wrote: > Hello! > > On a dual-dual RHEL4 machine I am doing some MP2 calculations that > have a serious IO overhead issues when other jobs need some IO. I > would like to add a software Raid 0 [after adding two identical > Seagate 7200.10 or 7200.11 drives] to this machine... if I knew how. > Could someone point me to some info on how to do this? > > Many thanks! > > John McKelvey -- Jozsef Csontos, Ph.D. (jozsefcsontos_at_creighton_dot_edu) Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Tue Feb 12 14:43:00 2008 From: "Florian Haberl Florian.Haberl-,-chemie.uni-erlangen.de" To: CCL Subject: CCL: Disk striping Message-Id: <-36273-080212130147-29463-MBu/GUPT2CGUxOzsj2MHCQ_._server.ccl.net> X-Original-From: Florian Haberl Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Date: Tue, 12 Feb 2008 18:08:31 +0100 MIME-Version: 1.0 Sent to CCL by: Florian Haberl [Florian.Haberl~~chemie.uni-erlangen.de] Hi, On Tuesday, 12. February 2008 16:44, John McKelvey jmmckel|gmail.com wrote: > Hello! > > On a dual-dual RHEL4 machine I am doing some MP2 calculations that have a > serious IO overhead issues when other jobs need some IO. I would like to > add a software Raid 0 [after adding two identical Seagate 7200.10 or > 7200.11drives] to this machine... if I knew how. Could someone point > me to some > info on how to do this? http://www.redhat.com/docs/manuals/enterprise/RHEL-4-Manual/sysadmin-guide/= ch-software-raid.html Another option is to buy a raid controller, for Raid0 also cheap ones are=20 enough (4ports SATA for around 100 Euros). Only thing you need is a PCIe=20 controller. > > Many thanks! > > John McKelvey Greetings, =46lorian =2D-=20 =2D------------------------------------------------------------------------= =2D----- Florian Haberl =20 Computer-Chemie-Centrum =20 Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) =E2=88=92 9131 =E2=88=92 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de =2D------------------------------------------------------------------------= =2D----- From owner-chemistry@ccl.net Tue Feb 12 15:36:01 2008 From: "David Hose anthrax_brothers*hotmail.com" To: CCL Subject: CCL: Formal charges Message-Id: <-36274-080212153420-31469-5zeSk1NdbwDpR5cdakfQfA^server.ccl.net> X-Original-From: "David Hose" Date: Tue, 12 Feb 2008 15:34:16 -0500 Sent to CCL by: "David Hose" [anthrax_brothers|-|hotmail.com] The formal charge is what you define in the properties dialogue box when you have selected an atom in your molecule (see the dropdown table towards the lower left [the default is "unspecified"]). From what I recall, unless you define the formal charge in this way, then nothing is displayed when requested. To be honest I don't use the formal charge option when setting calculations up, I just define the molecular charge and multiplicity in the calculations dialogue box before submitting the job, then extract the appropriate partial atomic charge afterwards for further analysis. Regards, Dave ----- But when I select labels and then formal charges nothing is displayed on the screen even after I run the calculations. Other charges show though (like mulliken etc). Also there is no option for formal charges in the display menu... On Feb 11, 2008 7:49 PM, David Hose anthrax_brothers ~~ hotmail.com wrote: Sent to CCL by: "David Hose" [anthrax_brothers===hotmail.com] If you want to display the charges on the 3D structure in Spartan, try this. From the Model menu select Labels. Depending upon your preferences, you might see the atom labels appear (default of white text on a green background, so the labels may be invisible if you have charged your background to white). Then select Configure... from the Model menu and select the appropriate radio button. If you haven't already discovered this, if you click the "P" icon in the Properties dialogue (under the Display menu), the charge of the atom selected will be added to the spreadsheet. Regards, Dave. > > Sent to CCL by: "Sina T reli" [sinatureli{:}gmail.com] > Hello, > > Is there any tool that will calculate formal charges on a molecular system and display it? I have tried spartan but couldnt figure how it displays formal charges though there is an option for it in the display menu... > > Thanks From owner-chemistry@ccl.net Tue Feb 12 17:51:01 2008 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli]-[gmail.com" To: CCL Subject: CCL: Formal charges Message-Id: <-36275-080212174814-1068-biu6mXxyruqyiyLnuwqQDw]-[server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_28982_18303613.1202852537882" Date: Tue, 12 Feb 2008 23:42:17 +0200 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli**gmail.com] ------=_Part_28982_18303613.1202852537882 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline yea in spartan it doesnt matter but in mopac you have to assign a correct charge for the system. and the systems I use are large systems so at some points I may mistakes in assigning charges and it gets frustrating. I taught maybe there could programs displaying the formal charge of the molecules according to lewis bonding system thanks tough On Feb 12, 2008 10:34 PM, David Hose anthrax_brothers*hotmail.com < owner-chemistry]![ccl.net> wrote: > > Sent to CCL by: "David Hose" [anthrax_brothers|-|hotmail.com] > The formal charge is what you define in the properties dialogue box when > you have selected an > atom in your molecule (see the dropdown table towards the lower left [the > default is > "unspecified"]). From what I recall, unless you define the formal charge > in this way, then nothing is > displayed when requested. > > To be honest I don't use the formal charge option when setting > calculations up, I just define the > molecular charge and multiplicity in the calculations dialogue box before > submitting the job, then > extract the appropriate partial atomic charge afterwards for further > analysis. > > Regards, > > Dave > > ----- > > But when I select labels and then formal charges nothing is displayed on > the screen even after I run > the calculations. Other charges show though (like mulliken etc). Also > there is no option for formal > charges in the display menu... > > On Feb 11, 2008 7:49 PM, David Hose anthrax_brothers ~~ hotmail.com chemistry*o*ccl.net> wrote: > > Sent to CCL by: "David Hose" [anthrax_brothers===hotmail.com] > If you want to display the charges on the 3D structure in Spartan, try > this. From the Model menu > select Labels. Depending upon your preferences, you might see the atom > labels appear (default of > white text on a green background, so the labels may be invisible if you > have charged your > background > to white). Then select Configure... from the Model menu and select the > appropriate radio button. > > If you haven't already discovered this, if you click the "P" icon in the > Properties dialogue (under the > Display menu), the charge of the atom selected will be added to the > spreadsheet. > > Regards, > > Dave. > > > > > Sent to CCL by: "Sina T reli" [sinatureli{:}gmail.com] > > Hello, > > > > Is there any tool that will calculate formal charges on a molecular > system and display it? I have > tried > spartan but couldnt figure how it displays formal charges though there is > an option for it in the > display menu... > > > > Thanks> > > ------=_Part_28982_18303613.1202852537882 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline yea in spartan it doesnt matter but in mopac you have to assign a correct charge for the system. and the systems I use are large systems so at some points I may mistakes in assigning charges and it gets frustrating. I taught maybe there could programs displaying the formal charge of the molecules according to lewis bonding system

thanks tough

On Feb 12, 2008 10:34 PM, David Hose anthrax_brothers*hotmail.com <owner-chemistry]![ccl.net> wrote:

Sent to CCL by: "David  Hose" [anthrax_brothers|-|hotmail.com]
The formal charge is what you define in the properties dialogue box when you have selected an
atom in your molecule (see the dropdown table towards the lower left [the default is
"unspecified"]).  From what I recall, unless you define the formal charge in this way, then nothing is
displayed when requested.

To be honest I don't use the formal charge option when setting calculations up, I just define the
molecular charge and multiplicity in the calculations dialogue box before submitting the job, then
extract the appropriate partial atomic charge afterwards for further analysis.

Regards,

Dave

-----

But when I select labels and then formal charges nothing is displayed on the screen even after I run
the calculations. Other charges show though (like mulliken etc). Also there is no option for formal
charges in the display menu...

On Feb 11, 2008 7:49 PM, David Hose anthrax_brothers ~~ hotmail.com <owner-
chemistry*o*ccl.net> wrote:

Sent to CCL by: "David  Hose" [anthrax_brothers===hotmail.com]
If you want to display the charges on the 3D structure in Spartan, try this.  From the Model menu
select Labels.  Depending upon your preferences, you might see the atom labels appear (default of
white text on a green background, so the labels may be invisible if you have charged your
background
to white).  Then select Configure... from the Model menu and select the appropriate radio button.

If you haven't already discovered this, if you click the "P" icon in the Properties dialogue (under the
Display menu), the charge of the atom selected will be added to the spreadsheet.

Regards,

Dave.

>
> Sent to CCL by: "Sina  T  reli" [sinatureli{:}gmail.com]
> Hello,
>
> Is there any tool that will calculate formal charges on a molecular system and display it? I have
tried
spartan but couldnt figure how it displays formal charges though there is an option for it in the
display menu...
>
> Thanks



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