From chemistry-request@ccl.net Wed Dec 31 13:12:44 2003 Received: from f1n1.spenet.wfu.edu (f1n1.sp2net.wfu.edu [152.17.8.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBVICCTC032136 for ; Wed, 31 Dec 2003 13:12:12 -0500 Received: from wfu.edu (salsbufr-PC.computer.wfu.edu [152.17.84.170]) by f1n1.spenet.wfu.edu (8.11.6p2/8.11.6) with ESMTP id hBVICCT41128 for ; Wed, 31 Dec 2003 13:12:12 -0500 Message-ID: <3FF3117C.8040200.-at-.wfu.edu> Disposition-Notification-To: freddie salsbury Date: Wed, 31 Dec 2003 13:12:12 -0500 From: freddie salsbury Organization: Wake Forest University User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry.-at-.ccl.net Subject: Periodic Boundary Conditions in Gaussian Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCler's -- About 1 month ago, I asked if anyone has had much success in G03 with PBC, because we seem unable to run a routine calc with diamond in 3D. Since they we have discovered that 1 or 2D calculations work fine, its just in 3D that things seem to break down. Has anyone succesfully ran a 3D calc with the PBC code in gaussian and with HF? If so would you share with us the input file? The one we've been using is attached below, along with our results. thanks for any assistance, cheers Fred ------------------------------- %chk=diamond2G.chk %mem=1024MB #HF/STO-3G PBC(NKPoint=48,CellRange=20) Pop(Full) diamond test 0 1 C 0.445875 0.445875 0.445875 C -0.445875 -0.445875 -0.445875 TV 1.7835 1.7835 0.0000 TV 1.7835 0.0000 1.7835 TV 0.0000 1.7835 1.7835 ---------------------------------- First, the gaussian output says it turns symmetry off (even if you turn it on, it cannot identify any symmetry). We varied the CellRange from 20 to 50 and obtained the following results: NClRep CellRange Energy Time (min) MaxNCR NMtPBC Convg 10 -74.8774038316 8.01 285 285 0.3482D-04 15 -74.8788470298 7.40 591 591 0.3388D-04 20 -79.7834971028 335.50 1357 1357 0.1513D-02 25 -77.9532971257 47.78 1717 2179 0.1892D-05 30 -78.4667709573 26.46 1721 3185 0.1067D-04 35 -78.8229423341 32.52 1721 4501 0.7331D-05 40 -78.9686326165 43.85 1721 6775 0.2602D-05 45 -86.8332484908 1479.41 1721 8903 0.2117D-03 50 -83.4676895141 1724.68 1721 11387(convergence failure) (the Cellrange=50 ended with an abnormal termination due to failure to converge) The ones that took a long time to run (20 and 45) not only had large Convg values in the SCF, but also in the population analysis had inequivalent carbons. Dr. Freddie Salsbury, Jr. Assistant Professor Department of Physics Wake Forest University Winston Salem, NC 27109 http://www.wfu.edu/~salsbufr http://csb.wfu.edu/(Center for Structural Biology) From chemistry-request@ccl.net Thu Jan 1 21:12:28 2004 Received: from mail.ccnu.edu.cn ([202.114.32.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i022BoTC025724 for ; Thu, 1 Jan 2004 21:11:54 -0500 Received: (eyou send program); Fri, 02 Jan 2004 10:11:45 +0800 Message-ID: <273009505.23065{at}mail.ccnu.edu.cn> Received: from 202.114.34.252 by 202.114.32.3 with HTTP; Fri, 02 Jan 2004 10:11:45 +0800 X-WebMAIL-MUA: [202.114.34.252] From: "" To: CHEMISTRY{at}ccl.net Date: Fri, 02 Jan 2004 10:11:45 +0800 Reply-To: "" Subject: ONIOM question? Content-Type: text/plain X-Spam-Status: No, hits=5.2 required=7.0 tests=DEAR_SOMETHING,MSG_ID_ADDED_BY_MTA_2,NO_REAL_NAME, RCVD_IN_RFCI version=2.55 X-Spam-Level: ***** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear sir, I am doing ONIOM calculation for an enzyme-ligand system including about 5100 atoms. Is it possible to do this calculation with ONIOM method in G03 program? When I try to do it, I got the following error information in the end of output file: -------------------------------------------------------------- I= 2535 IAn= 7 Valence= 4. JB= 1 J= 2536 IAn= 6 IBT= 1 Dist= 1.43D+00 JB= 2 J= 2540 IAn= 6 IBT= 1 Dist= 1.40D+00 JB= 3 J= 2544 IAn= 6 IBT= 1 Dist= 1.44D+00 JB= 4 J= 2532 IAn= 6 IBT= 1 Dist= 1.51D+00 Include all MM classes Bondstretch undefined between atoms 151 159 Bondstretch undefined between atoms 170 178 Bondstretch undefined between atoms 1031 1032 Bondstretch undefined between atoms 1032 1033 Bondstretch undefined between atoms 1267 1275 Bondstretch undefined between atoms 1479 1487 Bondstretch undefined between atoms 2020 2026 Angle bend undefined between atoms 150 151 159 Angle bend undefined between atoms 152 151 159 Angle bend undefined between atoms 169 170 178 Angle bend undefined between atoms 171 170 178 Angle bend undefined between atoms 1031 1032 1033 MM function not complete Error termination via Lnk1e in /usr/local/g03/l120.exe at Thu Jan 1 05:54:13 2004. Job cpu time: 0 days 6 hours 59 minutes 11.2 seconds. File lengths (MBytes): RWF= 731 Int= 0 D2E= 0 Chk= 93 Scr= 1 ---------------------------------------------------------- In fact, I have define those parameter in input files for G03. I found the following content in the beginning part of output file to confirm it: ----------------------------------------------------------------------- Read MM parameter file: Define 1.500 1 Include all MM classes MMInit generated parameter data with length LenPar=966946. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. ----------------------------------------------------------------------------- Could you please tell me what's wrong with it? Thank you! From chemistry-request@ccl.net Fri Jan 2 03:06:52 2004 Received: from mail.ccnu.edu.cn ([202.114.32.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0286ETC000564 for ; Fri, 2 Jan 2004 03:06:20 -0500 Received: (eyou send program); Fri, 02 Jan 2004 16:06:10 +0800 Message-ID: <273030770.24108!at!mail.ccnu.edu.cn> Received: from 202.114.34.252 by 202.114.32.3 with HTTP; Fri, 02 Jan 2004 16:06:10 +0800 X-WebMAIL-MUA: [202.114.34.252] From: "" To: CHEMISTRY!at!ccl.net Date: Fri, 02 Jan 2004 16:06:10 +0800 Reply-To: "" Subject: CCL: question about ONIOM Content-Type: text/plain X-Spam-Status: No, hits=5.2 required=7.0 tests=DEAR_SOMETHING,MSG_ID_ADDED_BY_MTA_2,NO_REAL_NAME, RCVD_IN_RFCI version=2.55 X-Spam-Level: ***** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear sir, I am doing ONIOM calculation for an enzyme-ligand system including about 5100 atoms. Is it possible to do this calculation with ONIOM method in G03 program? When I try to do it, I got the following error information in the end of output file: -------------------------------------------------------------- I= 2535 IAn= 7 Valence= 4. JB= 1 J= 2536 IAn= 6 IBT= 1 Dist= 1.43D+00 JB= 2 J= 2540 IAn= 6 IBT= 1 Dist= 1.40D+00 JB= 3 J= 2544 IAn= 6 IBT= 1 Dist= 1.44D+00 JB= 4 J= 2532 IAn= 6 IBT= 1 Dist= 1.51D+00 Include all MM classes Bondstretch undefined between atoms 151 159 Bondstretch undefined between atoms 170 178 Bondstretch undefined between atoms 1031 1032 Bondstretch undefined between atoms 1032 1033 Bondstretch undefined between atoms 1267 1275 Bondstretch undefined between atoms 1479 1487 Bondstretch undefined between atoms 2020 2026 Angle bend undefined between atoms 150 151 159 Angle bend undefined between atoms 152 151 159 Angle bend undefined between atoms 169 170 178 Angle bend undefined between atoms 171 170 178 Angle bend undefined between atoms 1031 1032 1033 MM function not complete Error termination via Lnk1e in /usr/local/g03/l120.exe at Thu Jan 1 05:54:13 2004. Job cpu time: 0 days 6 hours 59 minutes 11.2 seconds. File lengths (MBytes): RWF= 731 Int= 0 D2E= 0 Chk= 93 Scr= 1 ---------------------------------------------------------- In fact, I have define those parameter in input files for G03. I found the following content in the beginning part of output file to confirm it: ----------------------------------------------------------------------- Read MM parameter file: Define 1.500 1 Include all MM classes MMInit generated parameter data with length LenPar=966946. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. ----------------------------------------------------------------------------- Could you please tell me what's wrong with it? Thank you! From chemistry-request@ccl.net Fri Jan 2 03:56:36 2004 Received: from mail.ccnu.edu.cn ([202.114.32.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i028u2TC001099 for ; Fri, 2 Jan 2004 03:56:04 -0500 Received: (eyou send program); Fri, 02 Jan 2004 16:56:00 +0800 Message-ID: <273033760.24306)at(mail.ccnu.edu.cn> Received: from 202.114.34.252 by 202.114.32.3 with HTTP; Fri, 02 Jan 2004 16:56:00 +0800 X-WebMAIL-MUA: [202.114.34.252] From: "" To: CHEMISTRY)at(ccl.net Date: Fri, 02 Jan 2004 16:56:00 +0800 Reply-To: "" Subject: BU-NOSPAM / CCL: question about ONIOM Content-Type: text/plain X-Spam-Status: No, hits=5.2 required=7.0 tests=DEAR_SOMETHING,MSG_ID_ADDED_BY_MTA_2,NO_REAL_NAME, RCVD_IN_RFCI version=2.55 X-Spam-Level: ***** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear sir, I am doing ONIOM calculation for an enzyme-ligand system including about 5100 atoms. Is it possible to do this calculation with ONIOM method in G03 program? When I try to do it, I got the following error information in the end of output file: -------------------------------------------------------------- I= 2535 IAn= 7 Valence= 4. JB= 1 J= 2536 IAn= 6 IBT= 1 Dist= 1.43D+00 JB= 2 J= 2540 IAn= 6 IBT= 1 Dist= 1.40D+00 JB= 3 J= 2544 IAn= 6 IBT= 1 Dist= 1.44D+00 JB= 4 J= 2532 IAn= 6 IBT= 1 Dist= 1.51D+00 Include all MM classes Bondstretch undefined between atoms 151 159 Bondstretch undefined between atoms 170 178 Bondstretch undefined between atoms 1031 1032 Bondstretch undefined between atoms 1032 1033 Bondstretch undefined between atoms 1267 1275 Bondstretch undefined between atoms 1479 1487 Bondstretch undefined between atoms 2020 2026 Angle bend undefined between atoms 150 151 159 Angle bend undefined between atoms 152 151 159 Angle bend undefined between atoms 169 170 178 Angle bend undefined between atoms 171 170 178 Angle bend undefined between atoms 1031 1032 1033 MM function not complete Error termination via Lnk1e in /usr/local/g03/l120.exe at Thu Jan 1 05:54:13 2004. Job cpu time: 0 days 6 hours 59 minutes 11.2 seconds. File lengths (MBytes): RWF= 731 Int= 0 D2E= 0 Chk= 93 Scr= 1 ---------------------------------------------------------- In fact, I have define those parameter in input files for G03. I found the following content in the beginning part of output file to confirm it: ----------------------------------------------------------------------- Read MM parameter file: Define 1.500 1 Include all MM classes MMInit generated parameter data with length LenPar=966946. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. ----------------------------------------------------------------------------- Could you please tell me what's wrong with it? Thank you!