From owner-chemistry@ccl.net Tue Mar 31 02:18:00 2009 From: "uzma Mahmood mehmoodchemist:-:gmail.com" To: CCL Subject: CCL: SPSS software Message-Id: <-38976-090331010635-5040-vDpx8FKaL3zOS5txcu0HxQ++server.ccl.net> X-Original-From: "uzma Mahmood" Date: Tue, 31 Mar 2009 01:06:32 -0400 Sent to CCL by: "uzma Mahmood" [mehmoodchemist===gmail.com] To dear ALl respected and concern person heloo, some one can help me regrading SPSS software how i can find out the cross validation regression method in the Spss software i have v.17.0 because I am trying to apply this method for our date but not get the success for the exploration of the exact pattern thanks Mehmood Chemist From owner-chemistry@ccl.net Tue Mar 31 08:58:00 2009 From: "David Clark david.clark- -argentadiscovery.com" To: CCL Subject: CCL: Monitors for CADD/molecular modelling Message-Id: <-38977-090331074223-15630-G2JX8K8FaARCqplpaRFCnw . server.ccl.net> X-Original-From: "David Clark" Date: Tue, 31 Mar 2009 07:42:19 -0400 Sent to CCL by: "David Clark" [david.clark|argentadiscovery.com] Hi I've got an ageing SGI CRT display that may be coming to the end of its life. Can anyone suggest a modern replacement (LCD) that would be suitable for CADD/modelling tasks including stereo-vision with Stereographics? Many thanks David From owner-chemistry@ccl.net Tue Mar 31 09:33:00 2009 From: "Barbara Jagoda-Cwiklik barbara##fh.huji.ac.il" To: CCL Subject: CCL:G: Calculations methods Message-Id: <-38978-090331080937-18278-Jvh4dLCZ2f9MUBYQXu6POw-$-server.ccl.net> X-Original-From: Barbara Jagoda-Cwiklik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 31 Mar 2009 15:09:23 +0300 MIME-Version: 1.0 Sent to CCL by: Barbara Jagoda-Cwiklik [barbara,+,fh.huji.ac.il] On Mon, Mar 30, 2009 at 3:28 PM, noreya bestaoui noreya.bestaoui#gmail.com wrote: > Please, > Can anyone tell me how to use the counterpoise keyword and other options in > z-matrix of water and dimer (charge=0), to calculate BSSE correction in > G03 ? It will be greatly appreciated if someone could provide me with the > z-matrix of the input file for this. > I want to calculate using counterpoise keyword in G03. Dear Noreya Bestaoui, I'm not sure whether I get correctly what you mean by "other options" but I guess you want to calculate BSSE correction for water...water system using Z-matrix, right? The matrix for BSSE calculation for water dimer system looks as follows: 0 1 0 1 0 1 o 0.0 0.0 0.0 1 h 1 ho2 1 h 1 ho3 2 hoh3 1 o 1 oo4 3 ooh4 2 dih4 0 2 h 4 ho5 1 hoo5 2 dih5 0 2 h 4 ho6 5 hoh6 1 dih6 0 2 Variables: ho2 0.966691 ho3 0.966733 hoh3 104.202 oo4 2.915601 ooh4 107.614 dih4 116.024 ho5 0.972918 hoo5 6.677 dih5 -118.428 ho6 0.964893 hoh6 104.367 dih6 174.920 Some details (what is what and why) might be found in Gaussian's manual: http://www.gaussian.com/g_ur/k_counterpoise.htm Good luck, Basia -- Barbara Jagoda-Cwiklik, Ph.D The Fritz Haber Research Center for Molecular Dynamics Institute of Chemistry The Hebrew University of Jerusalem Jerusalem, ISRAEL e-mail: barbara###fh.huji.ac.il From owner-chemistry@ccl.net Tue Mar 31 11:01:01 2009 From: "Philippe Carbonniere philippe.carbonniere.:.univ-pau.fr" To: CCL Subject: CCL: ICCMSE 2009 symposium : Computational aspects of the modelling of vibrational properties Message-Id: <-38979-090331105453-26372-1J0ATu9zCQCMGWp+EdaQ+g|-|server.ccl.net> X-Original-From: Philippe Carbonniere Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 31 Mar 2009 16:52:24 +0200 MIME-Version: 1.0 Sent to CCL by: Philippe Carbonniere [philippe.carbonniere^-^univ-pau.fr] "Computational aspects of the modelling of vibrational properties of gases, liquids and solids" International symposium will be held in the conference: "Seventh International Conference of Computational Methods in Sciences and Engineering" (http://www.iccmse.org/) at Hotel Rodos Palace, Rodos, Crete, Greece. from September 29 to October 4, 2009. Submission of the short abstract is welcome for interested persons. Organizers : Philippe Carbonniere and Claude Pouchan, IPREM, Pau University, France and Mauro Causa, University "Federico II", Naples, Italy Contact philippe.carbonniere###univ-pau.fr Scope : Vibrational spectroscopy is a particularly powerful tool for non-destructive characterisation of molecular systems. Besides routine analysis in a wide range of domains (food science, archaeology, astrophysics, medicine),numerous applications in molecular science, such as speciation, conformational analysis, molecular design and reactivity monitoring, can be based on the modelling of vibrational effects. In recent years computational chemistry provides powerful tools for the modelling of such properties in the gas, liquid and solid phase although anharmonicity, resonances, environmental and dynamic effects render the problem non-trivial. Several computational aspects will be emphasised in the present symposium: the quality of the potential electronic surface, time-dependent and time-independent approaches to the study of vibration, the treatment of the condensed phases (solvent, surfaces and bulk), the computation of intensities and possible ways to overcome actual limitations due to the size of the treated systems. The performance of modern methods will be critically reviewed and their relative merit. -- Philippe Carbonnière, Maître de conférence Institut Pluridisciplinaire de Recherche en Environnement et Matériaux (IPREM, UMR5254) Laboratoire de Chimie Physique (LCP) F-64000 Pau Tel : 00 33 5 59 40 78 58 Fax : 00 33 5 59 40 78 62 From owner-chemistry@ccl.net Tue Mar 31 12:04:01 2009 From: "Warren DeLano warren[]delsci.com" To: CCL Subject: CCL: Monitors for CADD/molecular modelling Message-Id: <-38980-090331112448-6539-mhmGvCWKb97lUG8JeArnAA,+,server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C9B210.31307550" Date: Tue, 31 Mar 2009 07:47:11 -0700 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren||delsci.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C9B210.31307550 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable David,=20 120 Hz LCDs don't yet have the driver support they need for OpenGL, but = that may change sometime this quarter. In the meantime, there's the Zalman ZM-M220W, which both PYMOL and VMD = support. See the February 13th news entry on http://www.pymol.org about 3/4 of the way down. Cheers, Warren -----Original Message----- > From: owner-chemistry+warren=3D=3Ddelsci.com|*|ccl.net on behalf of David = Clark david.clark- -argentadiscovery.com Sent: Tue 3/31/2009 7:02 AM To: Warren DeLano Subject: CCL: Monitors for CADD/molecular modelling =20 Sent to CCL by: "David Clark" [david.clark|argentadiscovery.com] Hi I've got an ageing SGI CRT display that may be coming to the end of its = life. Can anyone suggest a modern replacement (LCD) that would be suitable for = CADD/modelling tasks including stereo-vision with Stereographics? Many thanks David -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------_=_NextPart_001_01C9B210.31307550-- From owner-chemistry@ccl.net Tue Mar 31 16:03:01 2009 From: "Andrei Leitao aleitao .. salud.unm.edu" To: CCL Subject: CCL: Monitors for CADD/molecular modelling Message-Id: <-38981-090331131245-30281-vZvWhOQx3glZfrQZuA3Gsw[a]server.ccl.net> X-Original-From: "Andrei Leitao" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=US-ASCII Date: Tue, 31 Mar 2009 10:09:43 -0600 Mime-Version: 1.0 Sent to CCL by: "Andrei Leitao" [aleitao**salud.unm.edu] As far as I know, there is no LCD monitor which has so high frequency = rate that allows you to see 3D. We tried to find a way to get the = stereographics working in Sybyl. The best we got was a linux system (it = may be Suse, Fedora, Ubuntu) with a really good graphics card that Tripos = has on a list (http://www.tripos.com/index.php?family=3Dmodules,SimplePage,= ,,&page=3Dlinux_graphics_cards) and an old 'traditional' monitor, in which = we had to play with the settings to get the best of the 3D cappability. I saw just one software that was able to use Zalman monitor (http://www.za= lman.co.kr/ENG/Main.asp) to perform 3D operations:=20 Best, Andrei Andrei Leitao, PhD Division of Biocomputing Health Sciences Center University of New Mexico http://biocomp.health.unm.edu/ >>> "David Clark david.clark- -argentadiscovery.com" 3/31/2009 5:42 AM >>> Sent to CCL by: "David Clark" [david.clark|argentadiscovery.com] Hi I've got an ageing SGI CRT display that may be coming to the end of its = life. Can anyone suggest a modern replacement (LCD) that would be suitable for = CADD/modelling tasks including stereo-vision with Stereographics? Many thanks David -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_message=20=20 Subscribe/Unsubscribe:=20=20=20 Job: http://www.ccl.net/jobs=20=20=20http://www.ccl.net/spammers.txt=20=20 From owner-chemistry@ccl.net Tue Mar 31 16:38:00 2009 From: "James Kubicki kubicki-#-geosc.psu.edu" To: CCL Subject: CCL: VASP "box and lattice vector scale in POSCAR" Message-Id: <-38982-090331140034-5565-K0H6fmH09svLzZmAjboa7w__server.ccl.net> X-Original-From: James Kubicki Content-Type: multipart/alternative; boundary="=====================_19529328==.ALT" Date: Tue, 31 Mar 2009 13:23:50 -0400 Mime-Version: 1.0 Sent to CCL by: James Kubicki [kubicki!A!geosc.psu.edu] --=====================_19529328==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed This is what I get for a 2x2x3 supercell of rutile. O Ti #Generated by CAR2POSCAR 1.00000000000000 9.18800000000000 0.00000000000000 0.00000000000000 0.00000000000000 9.18800000000000 0.00000000000000 0.00000000000000 0.00000000000000 8.87700000000000 48 24 Cartesian 1.40024995800000 1.40024995800000 0.00000000000000 #O1 1 3.19374990500000 3.19374990500000 0.00000000000000 #O2 2 0.89674997300000 3.69724988900000 1.47950005500000 #O3 3 3.69724988900000 0.89674997300000 1.47950005500000 #O4 4 1.40024995800000 1.40024995800000 2.95900011100000 #O5 5 3.19374990500000 3.19374990500000 2.95900011100000 #O6 6 0.89674997300000 3.69724988900000 4.43849992800000 #O7 7 3.69724988900000 0.89674997300000 4.43849992800000 #O8 8 1.40024995800000 1.40024995800000 5.91800022100000 #O9 9 3.19374990500000 3.19374990500000 5.91800022100000 #O10 10 0.89674997300000 3.69724988900000 7.39750003800000 #O11 11 3.69724988900000 0.89674997300000 7.39750003800000 #O12 12 1.40024995800000 5.99424982100000 0.00000000000000 #O13 13 3.19374990500000 7.78774976700000 0.00000000000000 #O14 14 0.89674997300000 8.29125022900000 1.47950005500000 #O15 15 3.69724988900000 5.49074983600000 1.47950005500000 #O16 16 1.40024995800000 5.99424982100000 2.95900011100000 #O17 17 3.19374990500000 7.78774976700000 2.95900011100000 #O18 18 0.89674997300000 8.29125022900000 4.43849992800000 #O19 19 3.69724988900000 5.49074983600000 4.43849992800000 #O20 20 1.40024995800000 5.99424982100000 5.91800022100000 #O21 21 3.19374990500000 7.78774976700000 5.91800022100000 #O22 22 0.89674997300000 8.29125022900000 7.39750003800000 #O23 23 3.69724988900000 5.49074983600000 7.39750003800000 #O24 24 5.99424982100000 1.40024995800000 0.00000000000000 #O25 25 7.78774976700000 3.19374990500000 0.00000000000000 #O26 26 5.49074983600000 3.69724988900000 1.47950005500000 #O27 27 8.29125022900000 0.89674997300000 1.47950005500000 #O28 28 5.99424982100000 1.40024995800000 2.95900011100000 #O29 29 7.78774976700000 3.19374990500000 2.95900011100000 #O30 30 5.49074983600000 3.69724988900000 4.43849992800000 #O31 31 8.29125022900000 0.89674997300000 4.43849992800000 #O32 32 5.99424982100000 1.40024995800000 5.91800022100000 #O33 33 7.78774976700000 3.19374990500000 5.91800022100000 #O34 34 5.49074983600000 3.69724988900000 7.39750003800000 #O35 35 8.29125022900000 0.89674997300000 7.39750003800000 #O36 36 5.99424982100000 5.99424982100000 0.00000000000000 #O37 37 7.78774976700000 7.78774976700000 0.00000000000000 #O38 38 5.49074983600000 8.29125022900000 1.47950005500000 #O39 39 8.29125022900000 5.49074983600000 1.47950005500000 #O40 40 5.99424982100000 5.99424982100000 2.95900011100000 #O41 41 7.78774976700000 7.78774976700000 2.95900011100000 #O42 42 5.49074983600000 8.29125022900000 4.43849992800000 #O43 43 8.29125022900000 5.49074983600000 4.43849992800000 #O44 44 5.99424982100000 5.99424982100000 5.91800022100000 #O45 45 7.78774976700000 7.78774976700000 5.91800022100000 #O46 46 5.49074983600000 8.29125022900000 7.39750003800000 #O47 47 8.29125022900000 5.49074983600000 7.39750003800000 #O48 48 0.00000000000000 0.00000000000000 0.00000000000000 #Ti1 49 2.29699993100000 2.29699993100000 1.47950005500000 #Ti2 50 0.00000000000000 0.00000000000000 2.95900011100000 #Ti3 51 2.29699993100000 2.29699993100000 4.43849992800000 #Ti4 52 0.00000000000000 0.00000000000000 5.91800022100000 #Ti5 53 2.29699993100000 2.29699993100000 7.39750003800000 #Ti6 54 0.00000000000000 4.59399986300000 0.00000000000000 #Ti7 55 2.29699993100000 6.89099979400000 1.47950005500000 #Ti8 56 0.00000000000000 4.59399986300000 2.95900011100000 #Ti9 57 2.29699993100000 6.89099979400000 4.43849992800000 #Ti10 58 0.00000000000000 4.59399986300000 5.91800022100000 #Ti11 59 2.29699993100000 6.89099979400000 7.39750003800000 #Ti12 60 4.59399986300000 0.00000000000000 0.00000000000000 #Ti13 61 6.89099979400000 2.29699993100000 1.47950005500000 #Ti14 62 4.59399986300000 0.00000000000000 2.95900011100000 #Ti15 63 6.89099979400000 2.29699993100000 4.43849992800000 #Ti16 64 4.59399986300000 0.00000000000000 5.91800022100000 #Ti17 65 6.89099979400000 2.29699993100000 7.39750003800000 #Ti18 66 4.59399986300000 4.59399986300000 0.00000000000000 #Ti19 67 6.89099979400000 6.89099979400000 1.47950005500000 #Ti20 68 4.59399986300000 4.59399986300000 2.95900011100000 #Ti21 69 6.89099979400000 6.89099979400000 4.43849992800000 #Ti22 70 4.59399986300000 4.59399986300000 5.91800022100000 #Ti23 71 6.89099979400000 6.89099979400000 7.39750003800000 #Ti24 72 At 07:58 AM 3/27/2009, you wrote: >Dear CCL Subscribers, > >I am trying to simulate rutile crystal. The box size for the crystal >has set as given below: >O Ti >1.000000000000 >16.66900000000 0.00000000000 0.000000000000 >0.000000000000 10.50300000000 0.000000000000 >0.000000000000 0.000000000000 10.52300000000 >48 24 >Cartesian >0.189999997616 1.621000051498 -3.956000089645 >-0.256999999285 -1.625000000000 1.985999941826 >. >. >. >The output I get in OUTCAR shows molecule broken in four small cubes >separated with gap even at zero number trajectory. It seems to me >that the BOX settings are not correct but it could be some other >problem too. I centered the crystal's coordinates and larger box >sizes but result were same. > >Any help to solve this problem would be of great help for me. > >Regards, > >Saurabh > > >Saurabh Agrawal, >PhD Student, >Department of Chemical and Bioprocess Engineering, >UCD, Belfield, >Dublin-4, Ireland James D. Kubicki 335 Deike Bldg. Dept. of Geosciences The Pennsylvania State University University Park, PA 16802 814-865-3951 814-863-7823 (Fax) --=====================_19529328==.ALT Content-Type: text/html; charset="us-ascii" This is what I get for a 2x2x3 supercell of rutile.

O  Ti        #Generated by CAR2POSCAR
    1.00000000000000
   9.18800000000000      0.00000000000000      0.00000000000000
   0.00000000000000      9.18800000000000      0.00000000000000
   0.00000000000000      0.00000000000000      8.87700000000000
    48    24
Cartesian
   1.40024995800000      1.40024995800000      0.00000000000000                   #O1        1
   3.19374990500000      3.19374990500000      0.00000000000000                   #O2        2
   0.89674997300000      3.69724988900000      1.47950005500000                   #O3        3
   3.69724988900000      0.89674997300000      1.47950005500000                   #O4        4
   1.40024995800000      1.40024995800000      2.95900011100000                   #O5        5
   3.19374990500000      3.19374990500000      2.95900011100000                   #O6        6
   0.89674997300000      3.69724988900000      4.43849992800000                   #O7        7
   3.69724988900000      0.89674997300000      4.43849992800000                   #O8        8
   1.40024995800000      1.40024995800000      5.91800022100000                   #O9        9
   3.19374990500000      3.19374990500000      5.91800022100000                   #O10      10
   0.89674997300000      3.69724988900000      7.39750003800000                   #O11      11
   3.69724988900000      0.89674997300000      7.39750003800000                   #O12      12
   1.40024995800000      5.99424982100000      0.00000000000000                   #O13      13
   3.19374990500000      7.78774976700000      0.00000000000000                   #O14      14
   0.89674997300000      8.29125022900000      1.47950005500000                   #O15      15
   3.69724988900000      5.49074983600000      1.47950005500000                   #O16      16
   1.40024995800000      5.99424982100000      2.95900011100000                   #O17      17
   3.19374990500000      7.78774976700000      2.95900011100000                   #O18      18
   0.89674997300000      8.29125022900000      4.43849992800000                   #O19      19
   3.69724988900000      5.49074983600000      4.43849992800000                   #O20      20
   1.40024995800000      5.99424982100000      5.91800022100000                   #O21      21
   3.19374990500000      7.78774976700000      5.91800022100000                   #O22      22
   0.89674997300000      8.29125022900000      7.39750003800000                   #O23      23
   3.69724988900000      5.49074983600000      7.39750003800000                   #O24      24
   5.99424982100000      1.40024995800000      0.00000000000000                   #O25      25
   7.78774976700000      3.19374990500000      0.00000000000000                   #O26      26
   5.49074983600000      3.69724988900000      1.47950005500000                   #O27      27
   8.29125022900000      0.89674997300000      1.47950005500000                   #O28      28
   5.99424982100000      1.40024995800000      2.95900011100000                   #O29      29
   7.78774976700000      3.19374990500000      2.95900011100000                   #O30      30
   5.49074983600000      3.69724988900000      4.43849992800000                   #O31      31
   8.29125022900000      0.89674997300000      4.43849992800000                   #O32      32
   5.99424982100000      1.40024995800000      5.91800022100000                   #O33      33
   7.78774976700000      3.19374990500000      5.91800022100000                   #O34      34
   5.49074983600000      3.69724988900000      7.39750003800000                   #O35      35
   8.29125022900000      0.89674997300000      7.39750003800000                   #O36      36
   5.99424982100000      5.99424982100000      0.00000000000000                   #O37      37
   7.78774976700000      7.78774976700000      0.00000000000000                   #O38      38
   5.49074983600000      8.29125022900000      1.47950005500000                   #O39      39
   8.29125022900000      5.49074983600000      1.47950005500000                   #O40      40
   5.99424982100000      5.99424982100000      2.95900011100000                   #O41      41
   7.78774976700000      7.78774976700000      2.95900011100000                   #O42      42
   5.49074983600000      8.29125022900000      4.43849992800000                   #O43      43
   8.29125022900000      5.49074983600000      4.43849992800000                   #O44      44
   5.99424982100000      5.99424982100000      5.91800022100000                   #O45      45
   7.78774976700000      7.78774976700000      5.91800022100000                   #O46      46
   5.49074983600000      8.29125022900000      7.39750003800000                   #O47      47
   8.29125022900000      5.49074983600000      7.39750003800000                   #O48      48
   0.00000000000000      0.00000000000000      0.00000000000000                   #Ti1      49
   2.29699993100000      2.29699993100000      1.47950005500000                   #Ti2      50
   0.00000000000000      0.00000000000000      2.95900011100000                   #Ti3      51
   2.29699993100000      2.29699993100000      4.43849992800000                   #Ti4      52
   0.00000000000000      0.00000000000000      5.91800022100000                   #Ti5      53
   2.29699993100000      2.29699993100000      7.39750003800000                   #Ti6      54
   0.00000000000000      4.59399986300000      0.00000000000000                   #Ti7      55
   2.29699993100000      6.89099979400000      1.47950005500000                   #Ti8      56
   0.00000000000000      4.59399986300000      2.95900011100000                   #Ti9      57
   2.29699993100000      6.89099979400000      4.43849992800000                   #Ti10     58
   0.00000000000000      4.59399986300000      5.91800022100000                   #Ti11     59
   2.29699993100000      6.89099979400000      7.39750003800000                   #Ti12     60
   4.59399986300000      0.00000000000000      0.00000000000000                   #Ti13     61
   6.89099979400000      2.29699993100000      1.47950005500000                   #Ti14     62
   4.59399986300000      0.00000000000000      2.95900011100000                   #Ti15     63
   6.89099979400000      2.29699993100000      4.43849992800000                   #Ti16     64
   4.59399986300000      0.00000000000000      5.91800022100000                   #Ti17     65
   6.89099979400000      2.29699993100000      7.39750003800000                   #Ti18     66
   4.59399986300000      4.59399986300000      0.00000000000000                   #Ti19     67
   6.89099979400000      6.89099979400000      1.47950005500000                   #Ti20     68
   4.59399986300000      4.59399986300000      2.95900011100000                   #Ti21     69
   6.89099979400000      6.89099979400000      4.43849992800000                   #Ti22     70
   4.59399986300000      4.59399986300000      5.91800022100000                   #Ti23     71
   6.89099979400000      6.89099979400000      7.39750003800000                   #Ti24     72



At 07:58 AM 3/27/2009, you wrote:
Dear CCL Subscribers,

I am trying to simulate rutile crystal. The box size for the crystal has set as given below:
O Ti
1.000000000000
16.66900000000 0.00000000000 0.000000000000
0.000000000000 10.50300000000 0.000000000000
0.000000000000 0.000000000000 10.52300000000
48 24
Cartesian
0.189999997616 1.621000051498 -3.956000089645
-0.256999999285 -1.625000000000 1.985999941826
.
.
.
The output I get in OUTCAR shows molecule broken in four small cubes separated with gap even at zero number trajectory. It seems to me that the BOX settings are not correct but it could be some other problem too. I centered the crystal's coordinates and larger box sizes but result were same.

Any help to solve this problem would be of great help for me.

Regards,

Saurabh


Saurabh Agrawal,
PhD Student,
Department of Chemical and Bioprocess Engineering,
UCD, Belfield,
Dublin-4, Ireland

James D. Kubicki
335 Deike Bldg.
Dept. of Geosciences
The Pennsylvania State University
University Park, PA 16802
814-865-3951
814-863-7823 (Fax)
--=====================_19529328==.ALT-- From owner-chemistry@ccl.net Tue Mar 31 17:13:02 2009 From: "Tim Dransfield timothy.dransfield:_:umb.edu" To: CCL Subject: CCL:G: Trouble with G98 PCM caculations, "Increase the MxTs"? Message-Id: <-38983-090331144215-11015-sWg8F8a/77EqIElgG4L4Xw^_^server.ccl.net> X-Original-From: "Tim Dransfield" Date: Tue, 31 Mar 2009 14:42:11 -0400 Sent to CCL by: "Tim Dransfield" [timothy.dransfield#,#umb.edu] Hello, everyone I've got an undergraduate struggling with a fairly ambitious computational project for his senior thesis, trying to model some transformations of nicotine in water solutions. He's running with the PCM model in B3LYP/6-31G**, and has a recurring problem that I can't find anywhere in the Gaussian manual. Unfortunately, all of my expertise is in gas phase calculations, and I'm at a loss. It's also frustrating, because a quick search of the CCL archives shows that this problem shows up annually... but there are no posted solutions! The problem begins when the PCM calculation fails due to insufficient tesserae. We use TSNUM to increase that value, and the job will often converge. However, in some recent cases with the larger basis set, we run into an error that we can't explain. A sample: Solvent: WATER Model : PCM/UAHF, Icomp = 2 Version: MATRIX INVERSION Cavity : ICOSAHEDRA with 320 initial tesserae ------------------------------------------------------------------------------ Nord Group Hybr Charge Alpha Radius Bonded to 1 CH sp2 0.08 1.20 1.815 C2 [s] N6 [d] 2 C sp3 0.08 1.20 1.500 C1 [s] C3 [s] C11 [s] 3 CH sp2 0.08 1.20 1.905 C2 [s] C4 [d] 4 CH sp2 0.08 1.20 1.815 C3 [d] C5 [s] 5 CH sp3 0.08 1.20 1.635 C4 [s] N6 [s] 6 N sp2 0.08 1.20 1.590 C1 [d] C5 [s] 11 CH sp3 0.08 1.20 1.680 C2 [s] C13 [s] 13 CH2 sp3 0.08 1.20 1.860 C11 [s] C16 [s] 16 CH2 sp3 0.08 1.20 1.680 C13 [s] C19 [s] 19 CH2 sp3 0.08 1.20 1.770 C16 [s] N22 [s] 22 NH sp3 0.08 1.20 1.590 C19 [s] C24 [s] 24 CH3 sp3 0.08 1.20 1.860 N22 [s] ------------------------------------------------------------------------------ Too many tesserae. Increase the MxTs. Error termination via Lnk1e in c:\program files\g98w\l502.exe. I do not know HOW to increase the MxTs, nor what a reasonable number might be. (This job was run with TSNUM=300) We would both very much appreciate any input from the list! Thanks in advance. Tim Timothy Dransfield Department of Chemistry UMass Boston timothy.dransfield-$-umb.edu From owner-chemistry@ccl.net Tue Mar 31 21:07:00 2009 From: "Andrew Dalke dalke^-^dalkescientific.com" To: CCL Subject: CCL: programming course for computational chemistry Message-Id: <-38984-090331210404-10194-cAKo4cL0exNZdJx2Vyy2nQ%server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 1 Apr 2009 02:03:49 +0200 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Andrew Dalke [dalke|,|dalkescientific.com] Just a reminder that my programming course, meant for computational chemists who want to be more effective at programming, will be on Leipzig, Germany on 27-29 April, 2009. This course will cover: - the basics of Python - using OEChem - plotting with matplotlib - working with XML - R and Python/R integration - using chemically-aware relational databases - web programming with Django, including embedding depictions and plots - interfacing with Excel All examples are drawn from cheminformatics and closely related fields. If you are interested, see http://dalkescientific.com/training/ or contact me directly. In addition, I plan to organize a similar course in Boston in September and to judge feasibility I would like feedback from anyone here who might be interested in such a course. Andrew dalke(_)dalkescientific.com