From owner-chemistry@ccl.net Mon Jul 24 01:55:00 2006 From: "Alessandro Contini alessandro.contini-*-unimi.it" To: CCL Subject: CCL:G: Solvation of organic molecules (with GROMACS) Message-Id: <-32227-060724014639-16382-zTVpz6486GKUP+dZpE+6jw!A!server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 7BIT Content-type: text/plain Date: Mon, 24 Jul 2006 07:46:17 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini/./unimi.it] Hi, PCM SP calculations could be done by g03 (all versions) by specifying the keywords: "scrf(pcm,read)" and SphereOnH=N in the "read" section, after molecule specifications, were N is the number of the atom to be explicited (i.e. your "transition hydrogen"). However for geometry optimization this keyword works with g03 versions post B.05 (a bug caused g03 to "forget" the explicited atom after the first iteration). Moreover, SP calculations and geometry optimization can be performed with PCM by specifing different topological models for atomic radii, such as radii=pauling or radii=UFF or radii=UAKS, as Luis suggested; such models consider all atoms to be explicit. Hope this help Alessandro Contini Il giorno ven, 21/07/2006 alle 12.50 -0400, ALBERT POATER TEIXIDOR albert.poater[A]udg.es ha scritto: > Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater-#-udg.es] > > Dear Gaussian users, > I receive this error message in PCM single point calculations of molecules > with nearly 100 atoms. There is a H atom, which is in the middle of two > other atoms. I have tested the options of PCM to converge it. And the > IPCM, which is too computationally expensive. Does anyone any idea to get > this type of calculation? Any help will be appreciated. > Best regards, > Albert > > > United Atom Topological Model (UA0 parameters set). > UA0: Hydrogen 55 is unbound. Keep it explicit at all point on the > UA0: potential energy surface to get meaningful results. > Error termination via Lnk1e in /estufa/soft/g03pedro/g03/l301.exe at Fri > Jul 21 03:17:13 2006. > Job cpu time: 0 days 0 hours 0 minutes 4.4 seconds. > File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 > Scr= 1 > > > Dr. Albert Poater Teixidor > c/Campus de Montilivi s/n > 972418358> > > From owner-chemistry@ccl.net Mon Jul 24 05:17:00 2006 From: "Mariusz Radon mariusz.radon,gmail.com" To: CCL Subject: CCL:G: gamess versus gaussian Message-Id: <-32228-060724051458-20197-VnuubneqKp0u71cLiWQJbA%x%server.ccl.net> X-Original-From: "Mariusz Radon" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 24 Jul 2006 11:14:47 +0200 MIME-Version: 1.0 Sent to CCL by: "Mariusz Radon" [mariusz.radon=-=gmail.com] Hi, Maybe this is due to incompatible default defintion of d functions in basis set used in variuos codes, i.e. cartesian vs spherical? I suggest you checking how many d functions you have (5 or 6) and eventually make it equal in gamess and gaussian. Best regards, Mariusz Radon On 7/24/06, tamar ansbacher etamar(!)fh.huji.ac.il wrote: > Sent to CCL by: "tamar ansbacher" [etamar*|*fh.huji.ac.il] > Hellow. > I am trying to do calculation on Xe containing molecules using GAMESS > and Gaussian. When using the very small -3-21G basis set, i get the same results in both codes. When using better basis sets, as DZVP or LJ18 ,I get deviations which are not negligible. (I am using the same kind of coordinates in both codes )The problem also appears when caculating Xe itself in the LJ18 basis set. What may be the source to this problem? > thanks > Tamar From owner-chemistry@ccl.net Mon Jul 24 06:35:00 2006 From: "Pablo Vitoria pablo.vitoria:-:ehu.es" To: CCL Subject: CCL:G: gamess versus gaussian Message-Id: <-32229-060724061039-8958-VNfoYoQgE48Ubj/nU8KJtg%server.ccl.net> X-Original-From: "Pablo Vitoria" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Mon, 24 Jul 2006 11:25:37 +0200 MIME-Version: 1.0 Sent to CCL by: "Pablo Vitoria" [pablo.vitoria|-|ehu.es] Hi Tamar, I assume that you are doing HF calculations, and then the source of the difference can only be the different use of cartesian or spherical d and/or f basis functions in Gamess and Gaussian. The default in Gamess is to use cartesian basis functions, whereas in Gaussian it depends on the basis set, although most of them use 5D (spherical). For 3-21G, the default is 6D (cartesian) which agrees with Gamess and that's why you get the same result with this basis set. For the other two basis sets, Gamess is using cartesian while Gaussian uses spherical basis functions, and the energies disagree. You can modify the defaults in both programs: - Gamess, with the ISPHER option in $CONTRL - Gaussian, with the 5D 7F (spherical) vs. 6D 10F (cartesian) keywords I hope this helps Best regards Pablo ----- Original Message ----- > From: "tamar ansbacher etamar(!)fh.huji.ac.il" To: "Vitoria, Pablo " Sent: Monday, July 24, 2006 2:09 AM Subject: CCL:G: gamess versus gaussian > Sent to CCL by: "tamar ansbacher" [etamar*|*fh.huji.ac.il] > Hellow. > I am trying to do calculation on Xe containing molecules using GAMESS > and Gaussian. When using the very small -3-21G basis set, i get the same > results in both codes. When using better basis sets, as DZVP or LJ18 ,I > get deviations which are not negligible. (I am using the same kind of > coordinates in both codes )The problem also appears when caculating Xe > itself in the LJ18 basis set. What may be the source to this problem? > thanks > Tamar> > > From owner-chemistry@ccl.net Mon Jul 24 08:36:00 2006 From: "Geoffrey Hutchison grh25=-=cornell.edu" To: CCL Subject: CCL: Molecular orbital energies plot Message-Id: <-32230-060724083109-9969-Nf7/pSDarmhUDSuEnDy/OQ!=!server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Sun, 23 Jul 2006 22:35:46 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Geoffrey Hutchison [grh25!=!cornell.edu] > Sent to CCL by: "Agalya Govindasamy" [agalya81(-)gmail.com] > I have molecular orbital energies of some systems and i want to > plot them > in a single figure and compare the energy levels. I am not able to do > this using Excel. The few times I've tried this in Excel, I assign each molecule a number -- so something like this: Molecule # Orbital Energy (eV) 1 -87.121 1 -87.120 ... 2 -80.205 2 -80.016 ... 3 -81.127 ... It's a pain, but it can be done. Honestly, I prefer doing plots in gnuplot or any of a range of other programs. Making real horizontal lines for the MO "ladder plot" in Excel is essentially impossible. If you increase the size, Excel increases the width of the line, making nearly degenerate states smear into each other too easily. Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruña Group http://abruna.chem.cornell.edu/ From owner-chemistry@ccl.net Mon Jul 24 09:17:00 2006 From: "Mpourmpakis Giannis gbourb . chemistry.uoc.gr" To: CCL Subject: CCL: Molecular orbital energies plot Message-Id: <-32231-060724063635-11262-71ka0UC3iFOIbTJDpLj1Zw_+_server.ccl.net> X-Original-From: Mpourmpakis Giannis Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 24 Jul 2006 12:57:05 +0300 MIME-Version: 1.0 Sent to CCL by: Mpourmpakis Giannis [gbourb*chemistry.uoc.gr] You can try the Origin program. Use the symbol "line" instead the square and you can plot the levels. Best regards, Giannis Agalya Govindasamy agalya81|,|gmail.com wrote: >Sent to CCL by: "Agalya Govindasamy" [agalya81(-)gmail.com] >I have molecular orbital energies of some systems and i want to plot them >in a single figure and compare the energy levels. I am not able to do >this using Excel. Could anyone please tell if there is any software to make >molecular orbital energy level plots.> > > > > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From owner-chemistry@ccl.net Mon Jul 24 11:14:01 2006 From: "rajesh c rajesh_chinagandham,rediffmail.com" To: CCL Subject: CCL: POAV Message-Id: <-32232-060724024137-5332-uWlhDK/N7XS3Dj6BU+iKgQ(-)server.ccl.net> X-Original-From: "rajesh c" Date: Mon, 24 Jul 2006 02:41:36 -0400 Sent to CCL by: "rajesh c" [rajesh_chinagandham**rediffmail.com] Hi people.. Is there some software available to do POAV analysis..? thanks in advance rajesh From owner-chemistry@ccl.net Mon Jul 24 14:06:00 2006 From: "huanglei huanglei++mail.utexas.edu" To: CCL Subject: CCL: Molecular orbital energies plot Message-Id: <-32233-060724123602-21258-J8MDJQxufTAXxR/YK0P7Aw-*-server.ccl.net> X-Original-From: "huanglei" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Mon, 24 Jul 2006 10:17:43 -0600 Mime-Version: 1.0 Sent to CCL by: "huanglei" [huanglei-x-mail.utexas.edu] You can try Origin(It should work, but it is not free.) or gnuplot(freeware, it is a little complex but you can find a lot of tutorial). Good luck! ======= 2006-07-23 08:52:33 ======= >Sent to CCL by: "Agalya Govindasamy" [agalya81(-)gmail.com] >I have molecular orbital energies of some systems and i want to plot them >in a single figure and compare the energy levels. I am not able to do >this using Excel. Could anyone please tell if there is any software to make >molecular orbital energy level plots.> > From owner-chemistry@ccl.net Mon Jul 24 16:24:00 2006 From: "Tapan Gupta tapanjames{=}yahoo.com" To: CCL Subject: CCL:G: Problem in Gaussian Opt+Freq calculation Message-Id: <-32234-060724153714-28851-uxeua0kMYjpkk31niygfAQ ~ server.ccl.net> X-Original-From: "Tapan Gupta" Date: Mon, 24 Jul 2006 15:37:14 -0400 Sent to CCL by: "Tapan Gupta" [tapanjames]-[yahoo.com] Dear Users, There is a problem. I have completed Opt+Freq Calculation using RHF and DFT(B3LYP) on a 14 atom problem which took 19 and 43 minutes respectively. When I am performing the same Opt+Freq Calculation using MP2 level of theory it gives the following messege in the output file after 2 Hrs, 34 minutes. Transformation cannot fit in the specified MaxDisk. Pls note that this messege comes in the output file after the optimization is complete and freq calc starts. I am not sending the other details because I think that this problem is related to Disk Space possibly. All the calculations using RHF and B3LYP level of theory have been completed successfully. After this I increased the memory from default 6MW to 400 MB and default Diskspace from 2000 MB to 8000 MB. After doing this the "Transformation cannot fit in the specified MaxDisk" error was gone but again the calculation stopped and the output file shows the following at the end. Inv2: IOpt= 1 Iter= 1 AM= 3.09D-15 Conv= 1.00D-12. Inverted reduced A of dimension 305 with in-core refinement. Saving first derivative matrices. End of Minotr Frequency-dependent properties file 721 does not exist. Leave Link 1002 at Tue Jul 25 00:35:37 2006, MaxMem= 52428800 cpu: 549.0 (Enter C:\G03W\l811.exe) MDV= 52428800. Form MO integral derivatives with frozen-active canonical formalism. MOERI=1 MOERIx=1 NAtoms= 14 NAtomA= 14 NAtomX= 14. Discarding MO integrals. MO basis two electron integral derivatives will not be stored on disk. IAlg= 3 DoFC=T DoPWx=T Debug=F. Frozen-core window: NFC= 8 NFV= 0. Reordered first order wavefunction length = 24626162 WUsed= 24133173 WInt= 467086 WEnd= 117170688 Dk804= 51375269. Dk1111= 0. Dk1112= 166438888. MaxDsk= 1048576000 LAFull= 24626162 DskLim= 1048576000. NUsed= 420303171. 300243171. 216570921. 207473984. 175824471. 154724796. In DefCFB: NBatch= 1, ICI= 29, ICA=121, LFMax= 21 Large arrays: LIAPS= 315810000, LIARS= 55266750 words. In StABat: MaxSiz= 15 MinSiz= 15 NAtomB= 10 DoIAMN: NPSUse= 1. writwa Can anybody pls tell me that what type of this error is?, why it is coming? , and what is the remedy for it. I am using Win XP and Gaussian 03 for Windows Please help me. Thanks in advance. Sincerely, Tapan From owner-chemistry@ccl.net Mon Jul 24 16:58:01 2006 From: "Silvina C. Pellegrinet pellegrinet[A]iquios.gov.ar" To: CCL Subject: CCL:G: does a raid improve the performance of gaussian for windows? Message-Id: <-32235-060724163213-8148-/dTV3o2+EyubDzykNYkCzw]-[server.ccl.net> X-Original-From: "Silvina C. Pellegrinet" Date: Mon, 24 Jul 2006 16:32:12 -0400 Sent to CCL by: "Silvina C. Pellegrinet" [pellegrinet+/-iquios.gov.ar] Hello! I'd be grateful if anyone could send me any information regarding the performance of gaussian for windows in a PC using a raid of two disks. Is it worth spending the money in two disks? what kind of raid should this be? The other main components i'm planning to buy include Intel D820 Dual core processor, Intel motherboard and 2x1GB DDR 400MHz RAM. Thank you very much in advance for your help! Regards Silvina From owner-chemistry@ccl.net Mon Jul 24 17:33:00 2006 From: "Shobe, David dshobe.:.sud-chemieinc.com" To: CCL Subject: CCL:G: Problem in Gaussian Opt+Freq calculation Message-Id: <-32236-060724171753-7852-NYAd8w2awG3ZSdlhihae2g~~server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 24 Jul 2006 23:17:42 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe#%#sud-chemieinc.com] Tapan, The Windows versions of Gaussian can't use a file bigger than 2GB. There is a trick which allows you to use more than one file for I/O operations. BEFORE the line beginning with "#", add the following line: %rwf=r1,240mw,r2,240mw,r3,240mw,r4,240mw,r5,240mw,r6,240mw,r7,240mw,r8,-1 Even with this line included (it tells Gaussian to split the read-write file into eight pieces of 240 megawords i.e. (8 x 240)MB), there is still a limit of 16GB total disk space usage. Hopefully the next edition of Gaussian will not have these limitations, but for now we are stuck with them. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry:_:ccl.net [mailto:owner-chemistry:_:ccl.net] Sent: Monday, July 24, 2006 4:28 PM To: Shobe, David Subject: CCL:G: Problem in Gaussian Opt+Freq calculation Sent to CCL by: "Tapan Gupta" [tapanjames]-[yahoo.com] Dear Users, There is a problem. I have completed Opt+Freq Calculation using RHF and DFT(B3LYP) on a 14 atom problem which took 19 and 43 minutes respectively. When I am performing the same Opt+Freq Calculation using MP2 level of theory it gives the following messege in the output file after 2 Hrs, 34 minutes. Transformation cannot fit in the specified MaxDisk. Pls note that this messege comes in the output file after the optimization is complete and freq calc starts. I am not sending the other details because I think that this problem is related to Disk Space possibly. All the calculations using RHF and B3LYP level of theory have been completed successfully. After this I increased the memory from default 6MW to 400 MB and default Diskspace from 2000 MB to 8000 MB. After doing this the "Transformation cannot fit in the specified MaxDisk" error was gone but again the calculation stopped and the output file shows the following at the end. Inv2: IOpt= 1 Iter= 1 AM= 3.09D-15 Conv= 1.00D-12. Inverted reduced A of dimension 305 with in-core refinement. Saving first derivative matrices. End of Minotr Frequency-dependent properties file 721 does not exist. Leave Link 1002 at Tue Jul 25 00:35:37 2006, MaxMem= 52428800 cpu: 549.0 (Enter C:\G03W\l811.exe) MDV= 52428800. Form MO integral derivatives with frozen-active canonical formalism. MOERI=1 MOERIx=1 NAtoms= 14 NAtomA= 14 NAtomX= 14. Discarding MO integrals. MO basis two electron integral derivatives will not be stored on disk. IAlg= 3 DoFC=T DoPWx=T Debug=F. Frozen-core window: NFC= 8 NFV= 0. Reordered first order wavefunction length = 24626162 WUsed= 24133173 WInt= 467086 WEnd= 117170688 Dk804= 51375269. Dk1111= 0. Dk1112= 166438888. MaxDsk= 1048576000 LAFull= 24626162 DskLim= 1048576000. NUsed= 420303171. 300243171. 216570921. 207473984. 175824471. 154724796. In DefCFB: NBatch= 1, ICI= 29, ICA=121, LFMax= 21 Large arrays: LIAPS= 315810000, LIARS= 55266750 words. In StABat: MaxSiz= 15 MinSiz= 15 NAtomB= 10 DoIAMN: NPSUse= 1. writwa Can anybody pls tell me that what type of this error is?, why it is coming? , and what is the remedy for it. I am using Win XP and Gaussian 03 for Windows Please help me. Thanks in advance. Sincerely, Tapanhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Mon Jul 24 21:29:00 2006 From: "Masahiko Suenaga alohascc+/-mbox.nc.kyushu-u.ac.jp" To: CCL Subject: CCL:G: Molecular orbital energies plot Message-Id: <-32237-060724212533-15441-U7BTm/qDUule9CV/ajahxQ|,|server.ccl.net> X-Original-From: Masahiko Suenaga Content-Type: text/plain; charset=us-ascii Date: Tue, 25 Jul 2006 10:25:19 +0900 Mime-Version: 1.0 Sent to CCL by: Masahiko Suenaga [alohascc__mbox.nc.kyushu-u.ac.jp] Try Facio. It's a freeware. http://www1.bbiq.jp/zzzfelis/Facio.html Facio can visualize MO levels as horizontal bars with their degeneracy. Please use "GAMESS/Gaussian MO Levels Graphical Viewer" in Tools menu. Best regards, Masahiko Suenaga, Ph.D. Department of Chemistry, Faculty of Sciences, Kyushu University, Japan > > ======= 2006-07-23 08:52:33 ======= > > >Sent to CCL by: "Agalya Govindasamy" [agalya81(-)gmail.com] > >I have molecular orbital energies of some systems and i want to plot them > >in a single figure and compare the energy levels. I am not able to do > >this using Excel. Could anyone please tell if there is any software to make > >molecular orbital energy level plots.> > > -- Masahiko Suenaga alohascc(_)mbox.nc.kyushu-u.ac.jp