From owner-chemistry@ccl.net Fri Jun 4 07:50:00 2010 From: "Matthew Tassell mtassell__gmail.com" To: CCL Subject: CCL: Problem with IRC Convergence Message-Id: <-42051-100604063603-12042-aaDUj9UZEfjEkzLElTdzkQ/a\server.ccl.net> X-Original-From: "Matthew Tassell" Date: Fri, 4 Jun 2010 06:36:02 -0400 Sent to CCL by: "Matthew Tassell" [mtassell{}gmail.com] Dear CCL I have been having problems trying to get an IRC calculation to work and i have tried everything that i know about to solve the problem. Below is the data from the first step away from a transition state. IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC Pt 1 Step number 1 out of a maximum of 60 Using modified Bulirsch-Stoer corrector interation. Using distance weighted interpolants to fit PES. Cycle 1 NS= 2 Cycle 2 NS= 4 Truncation Error = 0.001789004 Cycle 3 NS= 6 Truncation Error = 0.000008665 Cycle 4 NS= 8 Truncation Error = 0.000005185 Cycle 5 NS= 12 Truncation Error = 0.000001043 Cycle 6 NS= 16 Truncation Error = 0.000000149 Cycle 7 NS= 24 Truncation Error = 0.000000054 Cycle 8 NS= 32 Truncation Error = 0.000000007 BS completed in 8 cycles and 104 integration steps. SUMMARY OF CORRECTOR INTEGRATION: Original End Point Energy = -1661.292015 Corrected End Point Energy = -1661.292096 Old End-Start Dist. = 0.029095 New End-Start Dist. = 0.000011 New End-Old End Dist. = 0.029095 CORRECTOR INTEGRATION CONVERGENCE: Recorrection delta-x convergence threshold: 0.001826 Delta-x Convergence NOT Met IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC and this is the route section from my job %NProcshared=4 %MEM=3000MB #p irc=(MaxCycle=60,stepsize=1,tight,rcfc) M062X/6-311++G** scf=maxcyc=200 scrf=pcm guess=read geom=check I have tried playing around with the step size and convergence criteria to try and get a feel for nature of the TS but what ever i seem to do leads to the same error message, Delta-x Convergence NOT Met. If there is anybody who might like to offer a suggestion as to what is the problem i would be very gratefull Many thanks in advance From owner-chemistry@ccl.net Fri Jun 4 08:56:00 2010 From: "Lalitha Selvam lselvam|a|swin.edu.au" To: CCL Subject: CCL:G: Infrared calculation at different temperature Message-Id: <-42052-100603210035-9340-znYSo5wNpuANLnMbFF9RLA:-:server.ccl.net> X-Original-From: "Lalitha Selvam" Date: Thu, 3 Jun 2010 21:00:33 -0400 Sent to CCL by: "Lalitha Selvam" [lselvam ~~ swin.edu.au] Hi, I would like to calculate infrared and raman at different temperatures. I found keyword from gaussian manual and calculated the frequencies at 10K. however when i compare the frequencies of default temperature with 10k, it is same. The keywords used : #P B3LYP/6-31G* freq=raman Temperature=10.0 SCF=(Tight)IOP(6/7=3)IOP(6 /79=1) I am confused with what went wrong. I would greatly appreciate if anyone can help on this. Thanks Lalitha From owner-chemistry@ccl.net Fri Jun 4 09:35:00 2010 From: "Val Gillet v.gillet:_:sheffield.ac.uk" To: CCL Subject: CCL: Registrations closing: Sheffield chemoinformatics conference Message-Id: <-42053-100604075554-31373-QluyFHLPkH394n21KjIFWQ_+_server.ccl.net> X-Original-From: "Val Gillet" Date: Fri, 4 Jun 2010 07:55:52 -0400 Sent to CCL by: "Val Gillet" [v.gillet-$-sheffield.ac.uk] Fifth Joint Sheffield Conference on Chemoinformatics University of Sheffield, UK (MGMS and CSA Trust) 13th-15th July 2010 http://cisrg.shef.ac.uk/shef2010/ NOTE: registrations to close in 2 weeks on June 22nd. Val Gillet, v.gillet()sheffield.ac.uk, University of Sheffield From owner-chemistry@ccl.net Fri Jun 4 11:19:01 2010 From: "Rajagopalan S. r.subramanian{}ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: Infrared calculation at different temperature Message-Id: <-42054-100604103621-23503-qW3gB2xiEjHPIMjQ8YLRRg^_^server.ccl.net> X-Original-From: "Rajagopalan S." Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1; format="flowed" Date: Fri, 04 Jun 2010 15:56:49 +0200 MIME-Version: 1.0 Sent to CCL by: "Rajagopalan S." [r.subramanian-$-ipc.uni-stuttgart.de] Hi, fundamental frequencies are generally independent of temperature. May if you check the properties, which are related to heat (like enthalpy, Gibb's energy), you will notice some difference. hope it helps. On Thu, 3 Jun 2010 21:00:33 -0400 "Lalitha Selvam lselvam|a|swin.edu.au" wrote: > > Sent to CCL by: "Lalitha Selvam" [lselvam ~~ >swin.edu.au] > Hi, > > I would like to calculate infrared and raman at >different temperatures. I found > keyword from gaussian manual and calculated the >frequencies at 10K. however > when i compare the frequencies of default temperature >with 10k, it is same. > > The keywords used : > > #P B3LYP/6-31G* freq=raman Temperature=10.0 >SCF=(Tight)IOP(6/7=3)IOP(6 > /79=1) > > I am confused with what went wrong. I would greatly >appreciate if anyone can > help on this. > > Thanks > Lalitha > > > > -= 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/ > > From owner-chemistry@ccl.net Fri Jun 4 13:08:00 2010 From: "arslan ali arslanali1986++gmail.com" To: CCL Subject: CCL: energy calculations Message-Id: <-42055-100604102652-16564-gMJ4SwB2nBbgmQXD9fisEQ##server.ccl.net> X-Original-From: arslan ali Content-Type: multipart/alternative; boundary=00221534d4d307aad10488344025 Date: Fri, 4 Jun 2010 18:25:00 +0500 MIME-Version: 1.0 Sent to CCL by: arslan ali [arslanali1986:gmail.com] --00221534d4d307aad10488344025 Content-Type: text/plain; charset=ISO-8859-1 Hi can any body tell me what is the difference between energy minimization and geometry optimization? and their application to find out bond distances and/or strengths? 2ndly how powerful computer is required to run such calculation with DFT at B3LYP level with 6-31G* basis set for molecules like steroid etc regards and prayers Arslan --00221534d4d307aad10488344025 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable


Hi
=A0
can any body tell me what is the difference between energy minimizatio= n and geometry optimization? and their application to find out bond distanc= es and/or strengths?
=A0
2ndly how powerful computer is required to run such calculation with D= FT at B3LYP level with 6-31G* basis set for molecules like steroid etc
=A0
regards and prayers
Arslan


--00221534d4d307aad10488344025-- From owner-chemistry@ccl.net Fri Jun 4 13:43:00 2010 From: "Kalju Kahn kalju!=!chem.ucsb.edu" To: CCL Subject: CCL: Program to calculate chemical exchange rates from NMR spectra Message-Id: <-42056-100603211808-27509-Xepe/52SZEji7/uTnHkX+A^server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 3 Jun 2010 17:33:03 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju*|*chem.ucsb.edu] Hi Roby, I have some Mathematica scripts that accomplish this for two peaks via a solution to the McConnell. I probably need to tweak it for your special case. Let me know if this might be useful. Cheers, Kalju > > Sent to CCL by: Jacqueline Cawthray [jcawth01!A!gmail.com] > Hi > > You can try HypNMR by Peter Gans although it's not free. > > http://www.hyperquad.co.uk/hypnmr.htm > > Good luck > Jacquie > > Jacqueline Cawthray, Ph.D. > > Orvig Research Group > Department of Chemistry > University of British Columbia > 2036 Main Mall > Vancouver, BC, V6T 2A3 > Email: jcawth01%%chem.ubc.ca > > On Wed, Jun 2, 2010 at 9:53 AM, Roby Kurian > Roby_Kurian.%%.umit.maine.edu wrote: >> >> Sent to CCL by: "Roby Kurian" [Roby_Kurian/a\umit.maine.edu] >> >> Hi All, >> I was looking for a program to calculate chemical exchange rates from >> peak broadening in NMR spectra. I found an old paper (J.C.S.Dalton 1982) >> where they have calculated exchange rates using a program called Trigen >> three. I couldn't find any more >> info on this program or the method they used. >> >> Any suggestions much appreciated. >> >> Thanks in advance >> >> Roby Kurian >> >> >> >> Roby Kurian >> Graduate Student >> Dept of Chemistry >> University of Maine> >>      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> >> >> > > > > --> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Fri Jun 4 14:17:00 2010 From: "Gert Kruger kruger]=[ukzn.ac.za" To: CCL Subject: CCL:G: Amber input files for metal-amino acid complex in Gaussian Message-Id: <-42057-100604090729-17424-RRMErCD2jcYnjZ0vpqYuuA(!)server.ccl.net> X-Original-From: "Gert Kruger" Date: Fri, 4 Jun 2010 09:07:28 -0400 Sent to CCL by: "Gert Kruger" [kruger-$-ukzn.ac.za] Dear All, I want to know if AMBER (in Gaussian) can handle transition metals complexes of amino acids. If possible I would like t get more information on how to generate the input files. Thanks Gert Kruger From owner-chemistry@ccl.net Fri Jun 4 14:52:00 2010 From: "Rinderspacher, Berend (Cont, ARL/WMRD) berend.rinderspacher|,|us.army.mil" To: CCL Subject: CCL:G: Infrared calculation at different temperature (UNCLASSIFIED) Message-Id: <-42058-100604112400-31225-6KbbKG065RsW1lMxhy2UxQ(_)server.ccl.net> X-Original-From: "Rinderspacher, Berend (Cont, ARL/WMRD)" Content-class: urn:content-classes:message Content-Type: multipart/signed; protocol="application/x-pkcs7-signature"; micalg=SHA1; boundary="----=_NextPart_000_0167_01CB03D3.E810D0B0" Date: Fri, 4 Jun 2010 10:51:14 -0400 MIME-Version: 1.0 Sent to CCL by: "Rinderspacher, Berend (Cont, ARL/WMRD)" [berend.rinderspacher ~ us.army.mil] This is a multi-part message in MIME format. ------=_NextPart_000_0167_01CB03D3.E810D0B0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Classification: UNCLASSIFIED Caveats: NONE Why do you expect changes in the frequencies? You should only observe line-broadening due to temperature, not spectral shifts. -----Original Message----- Subject: CCL:G: Infrared calculation at different temperature Sent to CCL by: "Lalitha Selvam" [lselvam ~~ swin.edu.au] Hi, I would like to calculate infrared and raman at different temperatures. I found keyword from gaussian manual and calculated the frequencies at 10K. however when i compare the frequencies of default temperature with 10k, it is same. The keywords used : #P B3LYP/6-31G* freq=raman Temperature=10.0 SCF=(Tight)IOP(6/7=3)IOP(6 /79=1) I am confused with what went wrong. I would greatly appreciate if anyone can help on this. Thanks Lalithahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtClassification: UNCLASSIFIED Caveats: NONE ------=_NextPart_000_0167_01CB03D3.E810D0B0 Content-Type: application/x-pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="smime.p7s" MIAGCSqGSIb3DQEHAqCAMIACAQExCzAJBgUrDgMCGgUAMIAGCSqGSIb3DQEHAQAAoIIRlzCCA3Aw ggJYoAMCAQICAQUwDQYJKoZIhvcNAQEFBQAwWzELMAkGA1UEBhMCVVMxGDAWBgNVBAoTD1UuUy4g R292ZXJubWVudDEMMAoGA1UECxMDRG9EMQwwCgYDVQQLEwNQS0kxFjAUBgNVBAMTDURvRCBSb290 IENBIDIwHhcNMDQxMjEzMTUwMDEwWhcNMjkxMjA1MTUwMDEwWjBbMQswCQYDVQQGEwJVUzEYMBYG A1UEChMPVS5TLiBHb3Zlcm5tZW50MQwwCgYDVQQLEwNEb0QxDDAKBgNVBAsTA1BLSTEWMBQGA1UE AxMNRG9EIFJvb3QgQ0EgMjCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoCggEBAMAswfaNO6z/ PzzWcb64dCIH7HBBFfyrQOMHqsHD2J/+2kw6vz/I2Ch7SzYBwKxFJcPSDgqPhRhkED0aE3Aqb47X 3I2Ts0EPOCHNravCPSoF01cRNw3NjFH5k+PMRkkhjhS0zcsUPjjNcjHuqxLyZeo0LlZd/+5jdctt upE0/J7z9C0cvlDEQt9ZiP9qs/qobD3LVnFxBZa7n4DlgEVZZ0Gw68OtYKSAdQYXnA70Q+CZDhv7 f/WzzLKBgrH9MsG4vkGkZLVgOlpRMIzO3kEsGUdcSRBkuXSph0GvfW66wbihv2UxOgRn+bW7jpKK AGO4seaMOF+D/1DVO6Jda7IQzGMCAwEAAaM/MD0wHQYDVR0OBBYEFEl0uwxeunr+AlTve6DGlcYJ gHCWMAsGA1UdDwQEAwIBhjAPBgNVHRMBAf8EBTADAQH/MA0GCSqGSIb3DQEBBQUAA4IBAQCYkY0/ ici79cBpcyk7Nay6swh2PXAJkumERCEBfRR2G+5RbB2NFTctezFp9JpEuK9GzDT6I8sDJxnSgyF1 K+fgG5km3IRAleio0sz2WFxm7z9KlxCCHboKot1bBiudp2RO6y4BNaS0PxOtVeTVc6hpmxHxmPIx Hm9A1Ph4n46RoG9wBJBmqgYrzuF6krV94eDRluehOi3MsZ0fBUTth5nTTRpwOcEEDOV+2fGv1yAO 8SJ6JaRzmcw/pAcnlqiile2CuRbTnguHwsHyiPVi32jfx7xpUe2xXNxUVCkPCTmarAPB2wxNrm8K ehZJ8b+R0jiU0/aVLLdsyUK2jcqQjYXZMIIEQzCCAyugAwIBAgIDIrD/MA0GCSqGSIb3DQEBBQUA MF0xCzAJBgNVBAYTAlVTMRgwFgYDVQQKEw9VLlMuIEdvdmVybm1lbnQxDDAKBgNVBAsTA0RvRDEM MAoGA1UECxMDUEtJMRgwFgYDVQQDEw9ET0QgRU1BSUwgQ0EtMTkwHhcNMDkwNjI1MDAwMDAwWhcN MTExMjA5MjM1OTU5WjCBhDELMAkGA1UEBhMCVVMxGDAWBgNVBAoTD1UuUy4gR292ZXJubWVudDEM MAoGA1UECxMDRG9EMQwwCgYDVQQLEwNQS0kxEzARBgNVBAsTCkNPTlRSQUNUT1IxKjAoBgNVBAMT IVJJTkRFUlNQQUNIRVIuQkVSRU5ELkMuMTM3OTI0NjE5OTCBnzANBgkqhkiG9w0BAQEFAAOBjQAw gYkCgYEA54EBcw0kg7VnGaEVnsuDOExEL6Ji0Ba8ca20wDvgXnh0EDHTu0mgNcfTlTOnlJO7n8cw QfpmYeG5Pzdku6HSiILh04aie2txz/Vrtv8cwFKzHjejkhL6kJ/fvW6XqetYoCJYSsY+gZ+nmYVL DTdwgB9811VcP3Qmyub48rVr/dsCAwEAAaOCAWYwggFiMB8GA1UdIwQYMBaAFANtfbnAQe/2R68k HTuYHHQOjGTbMD8GA1UdHwQ4MDYwNKAyoDCGLmh0dHA6Ly9jcmwuZGlzYS5taWwvZ2V0Y3JsP0RP RCUyMEVNQUlMJTIwQ0EtMTkwDgYDVR0PAQH/BAQDAgUgMBYGA1UdIAQPMA0wCwYJYIZIAWUCAQsJ MB0GA1UdDgQWBBQFttboZjjGk/uvB9SoNWHwOxwE1DBtBggrBgEFBQcBAQRhMF8wOwYIKwYBBQUH MAKGL2h0dHA6Ly9jcmwuZGlzYS5taWwvZ2V0c2lnbj9ET0QlMjBFTUFJTCUyMENBLTE5MCAGCCsG AQUFBzABhhRodHRwOi8vb2NzcC5kaXNhLm1pbDArBgNVHREEJDAigSBiZXJlbmQucmluZGVyc3Bh Y2hlckB1cy5hcm15Lm1pbDAbBgNVHQkEFDASMBAGCCsGAQUFBwkEMQQTAlVTMA0GCSqGSIb3DQEB BQUAA4IBAQA2xvHZxvD8aoURtszedQy5wXgLUaCfOWmxCIZLRRPpGP4QgjrXofvwvvSSIntqsZn9 1NdSG1rnvqDxZAWSE+BpuTuH5L2FiUETQWhBniQ3q1smiW2cmiJZRG3S784VopznsACu76SNPZMJ Li8cDRhCuwx0DZ4csq+wDncGI6ii12BIdYOjnRhTt8sJ7UnUYPDqe7JyhOqmSyClWEwaZn6jMH7r j69TMxnuUcvIzy2vIpce+JkjOadVODhZE7MT4k/ps41WfZ98VBRbqpsNDM0hLvj3edsvtZhvTrg5 9AjU39zfLLFPQa5VMEvRhNtbV0wr0AU8Mu2GoLrQE4Fiy9mmMIIEjjCCA3agAwIBAgIDIrD7MA0G CSqGSIb3DQEBBQUAMF0xCzAJBgNVBAYTAlVTMRgwFgYDVQQKEw9VLlMuIEdvdmVybm1lbnQxDDAK BgNVBAsTA0RvRDEMMAoGA1UECxMDUEtJMRgwFgYDVQQDEw9ET0QgRU1BSUwgQ0EtMTkwHhcNMDkw NjI1MDAwMDAwWhcNMTExMjA5MjM1OTU5WjCBhDELMAkGA1UEBhMCVVMxGDAWBgNVBAoTD1UuUy4g R292ZXJubWVudDEMMAoGA1UECxMDRG9EMQwwCgYDVQQLEwNQS0kxEzARBgNVBAsTCkNPTlRSQUNU T1IxKjAoBgNVBAMTIVJJTkRFUlNQQUNIRVIuQkVSRU5ELkMuMTM3OTI0NjE5OTCBnzANBgkqhkiG 9w0BAQEFAAOBjQAwgYkCgYEA0IMjD6rNuyPWoSmi7SGI5xl5iZsxsjboOEMMGbL6Z87z6pralL+4 BLk/Jz9LGuYNd3TqZq3Nw7TNz951ovVbFp4Bp14FLGA3poNJjnZRNDnLdLsFEl1PhuYpgDHVW/J9 Q06szyToScW+gLMq1ecZPpBSchfnUn8YCGt7FD5Vh50CAwEAAaOCAbEwggGtMB8GA1UdIwQYMBaA FANtfbnAQe/2R68kHTuYHHQOjGTbMD8GA1UdHwQ4MDYwNKAyoDCGLmh0dHA6Ly9jcmwuZGlzYS5t aWwvZ2V0Y3JsP0RPRCUyMEVNQUlMJTIwQ0EtMTkwDgYDVR0PAQH/BAQDAgbAMBYGA1UdIAQPMA0w CwYJYIZIAWUCAQsJMB0GA1UdDgQWBBRV/12NniO2hz8gHYPJ2BUIuE/+9zBtBggrBgEFBQcBAQRh MF8wOwYIKwYBBQUHMAKGL2h0dHA6Ly9jcmwuZGlzYS5taWwvZ2V0c2lnbj9ET0QlMjBFTUFJTCUy MENBLTE5MCAGCCsGAQUFBzABhhRodHRwOi8vb2NzcC5kaXNhLm1pbDBLBgNVHREERDBCgSBiZXJl bmQucmluZGVyc3BhY2hlckB1cy5hcm15Lm1pbKAeBgorBgEEAYI3FAIDoBAMDjEzNzkyNDYxOTlA bWlsMBsGA1UdCQQUMBIwEAYIKwYBBQUHCQQxBBMCVVMwKQYDVR0lBCIwIAYKKwYBBAGCNxQCAgYI KwYBBQUHAwIGCCsGAQUFBwMEMA0GCSqGSIb3DQEBBQUAA4IBAQBl6Ff0PK4loKmUVYLFmTFIQyOd bSh1xIrom8+GR4NLIjnRLtdxORlVZfba0RH95a0/PJJQiE/cuf3KB3wzYyoxy1ze6pi3qjNGgWlW 6iHBdmEBKms3sWQVS9bE/FqKLKIT036fY2j+TCfDwiuLSb820e/JNMQYNA9wd+UcxSvdy9FFAe5O Km1BzxGtdsQcMuaACPGEzPtPl+1QtFx4VZRQ2+kQZXAGZv/w+D/J5B4uBxbA2trSxZJ8i/K5+tRt CRWnPVXfmXZbA5+XgR13ZLjadZPdKVl68dv4m9aGW96H6PL8aPuG4iz/txS6gdOqmK1KmYOMJPNw K8zQ//m1Pu9OMIIFRjCCBC6gAwIBAgIBKTANBgkqhkiG9w0BAQUFADBbMQswCQYDVQQGEwJVUzEY MBYGA1UEChMPVS5TLiBHb3Zlcm5tZW50MQwwCgYDVQQLEwNEb0QxDDAKBgNVBAsTA1BLSTEWMBQG A1UEAxMNRG9EIFJvb3QgQ0EgMjAeFw0wODA0MjMyMTAzMDZaFw0xNDA0MjMyMDAzMDZaMF0xCzAJ BgNVBAYTAlVTMRgwFgYDVQQKEw9VLlMuIEdvdmVybm1lbnQxDDAKBgNVBAsTA0RvRDEMMAoGA1UE CxMDUEtJMRgwFgYDVQQDEw9ET0QgRU1BSUwgQ0EtMTkwggEiMA0GCSqGSIb3DQEBAQUAA4IBDwAw ggEKAoIBAQCquadeBhCmM9ZLS6On02wtefnXHHh82jw8LVsmc0EWTWQp+m0v9RULSFEOBsz05IvJ KVH3P7wnd/qV6pIk87CnDtRpr/K5N4eg/CeIGiDl4EtP8oFVAhR/TTuk4e2golS54hQIAfRcXIh3 X1xGQqR8HFRzF0SW6thTVP+/x323aXlyo2TV/ujhhICzGsJInk3PvZc8wIFVKMNIZEkwgBEhpOrV Xl9YibRX7sab9YNrWJfbm6t94De+vWjY3Ugilv94tnven3LmcXSCOrUM/iyd/e0qZrI036HKLCC7 nSRL75WVvCicwlebEYL1nadM3anyE8GvAhzpF1YW8K6obgsbAgMBAAGjggIRMIICDTAOBgNVHQ8B Af8EBAMCAYYwHwYDVR0jBBgwFoAUSXS7DF66ev4CVO97oMaVxgmAcJYwHQYDVR0OBBYEFANtfbnA Qe/2R68kHTuYHHQOjGTbMAwGA1UdJAQFMAOAAQAwEgYDVR0TAQH/BAgwBgEB/wIBADBXBgNVHSAE UDBOMAsGCWCGSAFlAgELBTALBglghkgBZQIBCwkwCwYJYIZIAWUCAQsKMAsGCWCGSAFlAgELEjAL BglghkgBZQIBCxMwCwYJYIZIAWUCAQsUMD8GA1UdHwQ4MDYwNKAyoDCGLmh0dHA6Ly9jcmwuZGlz YS5taWwvZ2V0Y3JsP0RvRCUyMFJvb3QlMjBDQSUyMDIwgf4GCCsGAQUFBwEBBIHxMIHuMD8GCCsG AQUFBzAChjNodHRwOi8vY3JsLmRpc2EubWlsL2dldElzc3VlZFRvP0RvRCUyMFJvb3QlMjBDQSUy MDIwIAYIKwYBBQUHMAGGFGh0dHA6Ly9vY3NwLmRpc2EubWlsMIGIBggrBgEFBQcwAoZ8bGRhcDov L2NybC5nZHMuZGlzYS5taWwvY24lM2REb0QlMjBSb290JTIwQ0ElMjAyJTJjb3UlM2RQS0klMmNv dSUzZERvRCUyY28lM2RVLlMuJTIwR292ZXJubWVudCUyY2MlM2RVUz9jQUNlcnRpZmljYXRlO2Jp bmFyeTANBgkqhkiG9w0BAQUFAAOCAQEAblkGi+5rkf+Xt69e+sCyAoBeq0MNtmUVS36uVpAxV1j8 V8GOKY+scDCaUTphdRYY/XbsnwAImP9komD3nl3Q2/KQGIW0ybEHSmdy7e3kC7zbvyLiB8xNuH5K wcuJ5I0EeK8hnsFo6pubpceN9TKs2AqMetByPiBnEDm6iSOn1JmlaE6EBekhEHzjsZJZBXrohI5e 12rU+XslxkJ4vI2yi1St0be7wU02oWhn9xEO+a51Izes6LPMSi23ZhhzY02c8PjhlzbNJhxZCFCz 5QNxdYBcHBI7TeJXKGS6V22301GWqAAO8XoLyfcvwnzQwzS+/zX4iwIH61ACKWuKdEmXJTGCAsAw ggK8AgEBMGQwXTELMAkGA1UEBhMCVVMxGDAWBgNVBAoTD1UuUy4gR292ZXJubWVudDEMMAoGA1UE CxMDRG9EMQwwCgYDVQQLEwNQS0kxGDAWBgNVBAMTD0RPRCBFTUFJTCBDQS0xOQIDIrD7MAkGBSsO AwIaBQCgggGyMBgGCSqGSIb3DQEJAzELBgkqhkiG9w0BBwEwHAYJKoZIhvcNAQkFMQ8XDTEwMDYw NDE0NTEzN1owIwYJKoZIhvcNAQkEMRYEFHHsibQULJvTOJt3zij8eNSkeqrFMGcGCSqGSIb3DQEJ DzFaMFgwCgYIKoZIhvcNAwcwDgYIKoZIhvcNAwICAgCAMA0GCCqGSIb3DQMCAgFAMAcGBSsOAwIH MA0GCCqGSIb3DQMCAgEoMAcGBSsOAwIaMAoGCCqGSIb3DQIFMHMGCSsGAQQBgjcQBDFmMGQwXTEL MAkGA1UEBhMCVVMxGDAWBgNVBAoTD1UuUy4gR292ZXJubWVudDEMMAoGA1UECxMDRG9EMQwwCgYD VQQLEwNQS0kxGDAWBgNVBAMTD0RPRCBFTUFJTCBDQS0xOQIDIrD/MHUGCyqGSIb3DQEJEAILMWag ZDBdMQswCQYDVQQGEwJVUzEYMBYGA1UEChMPVS5TLiBHb3Zlcm5tZW50MQwwCgYDVQQLEwNEb0Qx DDAKBgNVBAsTA1BLSTEYMBYGA1UEAxMPRE9EIEVNQUlMIENBLTE5AgMisP8wDQYJKoZIhvcNAQEB BQAEgYCPUr1MGoIF3CrDIdCghwmpBig/ure9IaADTYnEPWewcyXvxnikt0AdvbpyMlDSxI6vaCCN wuNoDSgfr1ti59sZ0cVSOE9HxikozTy/nkbKRpNMoxSzBhIYqm7sH7aR8TIEht03Mn9vrF/W7++4 gUB9WpHRBclDZ2E+bYbawFhUcwAAAAAAAA== ------=_NextPart_000_0167_01CB03D3.E810D0B0-- From owner-chemistry@ccl.net Fri Jun 4 15:28:00 2010 From: "partha kundu partha1kundu|-|yahoo.com" To: CCL Subject: CCL:G: GAR2PED Message-Id: <-42059-100604064114-19962-nq+HtoafNJs8COnwPoHZuA]^[server.ccl.net> X-Original-From: "partha kundu" Date: Fri, 4 Jun 2010 06:41:09 -0400 Sent to CCL by: "partha kundu" [partha1kundu^^^yahoo.com] Dear all, I am trying to do PED calculation using GAR2PED. According to the previous suggestions I typed ./pullarc FILENAME (without ./ this is not working even if I add path). But it is producing only FILENAME.xyz file instead of .arch file. My input for gaussian is following. %chk=t.chk %mem=6MW %nproc=1 #p freq=raman b3lyp/3-21g geom=allcheck guess=read Could someone help me? Thanks in advance. Partha From owner-chemistry@ccl.net Fri Jun 4 22:42:01 2010 From: "Close, David M. CLOSED_+_mail.etsu.edu" To: CCL Subject: CCL: energy calculations Message-Id: <-42060-100604151819-28620-8MtSGoS+eigd+zJ5jcvGYQ-.-server.ccl.net> X-Original-From: "Close, David M." Content-Class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CB0416.7147D926" Date: Fri, 4 Jun 2010 14:47:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED**mail.etsu.edu] ------_=_NextPart_001_01CB0416.7147D926 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Arslan: They go together. An optimization routine is instructed to make small change in the geometry of a molecule. If this effort results in a decrease energy, the routine continues until the change in energy is below some set criteria. The real question is does this procedure produce the global minimum? No, often one gets stuck on a local minimum. This happens when the potential energy surface is rather flat, and in this case small changes in geometry don't produce changes in the energy. But there are ways to get out of these local minima and to continue the search for the global minima. I think a steroid involves 4 fused 6-membered rings? And the rings are flat? This should be easy for a desktop workstation. Regards, Dave Close. =20 > From: owner-chemistry+closed=3D=3Detsu.edu[A]ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu[A]ccl.net] On Behalf Of = arslan ali arslanali1986++gmail.com Sent: Friday, June 04, 2010 9:25 AM To: Close, David M. Subject: CCL: energy calculations =20 =20 Hi =20 can any body tell me what is the difference between energy minimization and geometry optimization? and their application to find out bond distances and/or strengths? =20 2ndly how powerful computer is required to run such calculation with DFT at B3LYP level with 6-31G* basis set for molecules like steroid etc =20 regards and prayers Arslan =20 =20 ------_=_NextPart_001_01CB0416.7147D926 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Arslan:

  They go together.  An optimization routine is instructed to make small change in the geometry of a molecule.  If = this effort results in a decrease energy, the routine continues until the = change in energy is below some set criteria.   The real question is does = this procedure produce the global minimum?  No, often one gets stuck on = a local minimum.  This happens when the potential energy surface is rather = flat, and in this case small changes in geometry don’t produce changes = in the energy.  But there are ways to get out of these local minima and to continue the search for the global minima.

  I think a steroid involves 4 fused 6-membered = rings?   And the rings are flat?  This should be easy for a desktop = workstation.

Regards, Dave Close.

 

From:= owner-chemistry+closed=3D=3Detsu.edu[A]ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu[A]ccl.net] On Behalf Of = arslan ali arslanali1986++gmail.com
Sent: Friday, June 04, 2010 9:25 AM
To: Close, David M.
Subject: CCL: energy calculations

 

 

Hi

 

can any body tell me what is the difference between = energy minimization and geometry optimization? and their application to find = out bond distances and/or strengths?

 

2ndly how powerful computer is required to run such calculation with DFT at B3LYP level with 6-31G* basis set for molecules = like steroid etc

 

regards and prayers

Arslan

 

 

------_=_NextPart_001_01CB0416.7147D926-- From owner-chemistry@ccl.net Fri Jun 4 23:52:00 2010 From: "Mark Onyango mark.onyango-*-tg.fh-giessen.de" To: CCL Subject: CCL: energy calculations Message-Id: <-42061-100604151336-23979-GPH5W31muhsPP80HCqS1qQ-x-server.ccl.net> X-Original-From: Mark Onyango Content-Type: multipart/alternative; boundary="------------030404030303020009050508" Date: Fri, 04 Jun 2010 20:36:05 +0200 MIME-Version: 1.0 Sent to CCL by: Mark Onyango [mark.onyango(0)tg.fh-giessen.de] This is a multi-part message in MIME format. --------------030404030303020009050508 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Am 04.06.2010 15:25, schrieb arslan ali arslanali1986++gmail.com: > > > Hi > > can any body tell me what is the difference between energy > minimization and geometry optimization? and their application to find > out bond distances and/or strengths? > 2ndly how powerful computer is required to run such calculation with > DFT at B3LYP level with 6-31G* basis set for molecules like steroid etc > regards and prayers > Arslan > > Hello Arslan, an energy minimization is merely a single-point calculation, meaning minimizing the energy in a self-consistent field calculation at the given geometry. to find the geometry that resembles a minimum on the potential surface you have to start a geometry optimization. that means a series of scf calculations will take place followed by the calculation of the forces resulting from the new electron distribution and afterwards rearranging the atoms accordingly. this is what you want to do if you want to find a minimum structure with optimized bond lengths and angles. i suggest you read this topic up in a book such as "Introduction to Computational Chemistry" by Frank Jensen or "Modern Quantum Chemistry" by Szabo and Ostlund for further questions. With regards, Mark Onyango --------------030404030303020009050508 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Am 04.06.2010 15:25, schrieb arslan ali arslanali1986++gmail.com:


Hi
 
can any body tell me what is the difference between energy minimization and geometry optimization? and their application to find out bond distances and/or strengths?
 
2ndly how powerful computer is required to run such calculation with DFT at B3LYP level with 6-31G* basis set for molecules like steroid etc
 
regards and prayers
Arslan


Hello Arslan,

an energy minimization is merely a single-point calculation, meaning minimizing the energy in a self-consistent field calculation at the given geometry. to find the geometry that resembles a minimum on the potential surface you have to start a geometry optimization. that means a series of  scf calculations will take place followed by the calculation of the forces resulting from the new electron distribution and afterwards rearranging the atoms accordingly. this is what you want to do if you want to find a minimum structure with optimized bond lengths and angles.

i suggest you read this topic up in a book such as "Introduction to Computational Chemistry" by Frank Jensen or "Modern Quantum Chemistry" by Szabo and Ostlund for further questions.

With regards,

Mark Onyango
--------------030404030303020009050508--