From chemistry-request@ccl.net Fri May 7 07:59:28 2004 Received: from upstate.edu (gw4.upstate.edu [139.127.9.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i47CxPkh007627 for ; Fri, 7 May 2004 07:59:28 -0500 Received: from HSCHOSP-MTA by upstate.edu with Novell_GroupWise; Fri, 07 May 2004 09:01:08 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.4 Date: Fri, 07 May 2004 09:00:58 -0400 From: "Michael Chen" To: Subject: "Constarint failure" in NAMD Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Spam-Status: No, hits=1.0 required=7.5 tests=ALUSSINAN_5 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, Everyone, Hope all is well for you. It was so strange for me that when I used "run" command, I got lots of ERROR messages as following: ERROR: Constraint failure in RATTLE algorithm for atom 2264! ERROR: Constraint failure; simulation has become unstable. What did this mean? How should I kill this problem? I minimized my system for quite a long time, and I turned the constraint on for the Ca atoms. Thanks for the answer. May you have a nice day. ***************************************************** Michael Chen Department of Biochemistry SUNY Upstate Medical University 750 East Adams Street Syracuse, NY 13210 USA ***************************************************** From chemistry-request@ccl.net Fri May 7 11:18:27 2004 Received: from sandesh.iitkgp.ernet.in ([203.197.98.27]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i47GIOkh014001 for ; Fri, 7 May 2004 11:18:25 -0500 Received: from cts.iitkgp.ernet.in (localhost [127.0.0.1]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id VAA12372 for ; Fri, 7 May 2004 21:39:48 -0500 (GMT) X-Authentication-Warning: iitkgp.iitkgp.ernet.in: iscan owned process doing -bs Received: from localhost (utpal@localhost) by cts.iitkgp.ernet.in (8.11.6/8.11.6) with ESMTP id i47FgEb12987 for ; Fri, 7 May 2004 21:12:17 +0530 Date: Fri, 7 May 2004 21:12:14 +0530 (IST) From: utpal sarkar To: chemistry[at]ccl.net Subject: Gaussian Help Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL users, I want to study (sodium trifulride or cisium trifulride). B3LYP level of calculation I am doing to explore the corresponding potential energy surface (PES). I want to choose the LANL2DZ effective core potential Na and Cs, while the standard 6-31G(d,p) basis sets will be employed for the rest of the atoms. So what keyword I have to put in the root section? I will be highly obliged if you kindly mention the whole root section. Thanking you in advance. With regards Utpal ***************************************** This Mail is Certified to be Virus Free. CIC Network Security Group, IIT Kharagpur ***************************************** From chemistry-request@ccl.net Fri May 7 20:50:34 2004 Received: from mxout4.cac.washington.edu (mxout4.cac.washington.edu [140.142.33.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i481oXkh002136 for ; Fri, 7 May 2004 20:50:33 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.32.139]) by mxout4.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i481qKUr006498 for ; Fri, 7 May 2004 18:52:25 -0700 Received: from u.washington.edu (konga.chem.washington.edu [128.95.128.222]) (authenticated bits=0) by smtp.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i481qKXQ014207 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Fri, 7 May 2004 18:52:20 -0700 Message-ID: <409C3D4A.9030105_at_u.washington.edu> Date: Fri, 07 May 2004 18:52:10 -0700 From: Carsten Detering User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: gaussian03 + PES scan + solvent Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear fellow CClers, I am currently calculating a PES scan for an intramolecular, base-catalyzed proton transfer. In order to do so, I attached the proton to a dummy atom, and this dummy atom is in turn attached to another dummy atom, so that the proton is rectangular to the latter. To scan the surface, I move the dummy atom in the Y-axis, and the proton in the X-axis, so that it gives me a rectangular grid with energy values. I use Gaussian03 to perform this task. Since I want to perform a relaxed scan, I use the opt=z-matriz, and add the two parameters to scan at the end of the input file, like so: #HF/STO-3G opt=z-matrix test ... ... ... R15 0.7 S 10 0.25 R16 0.01 S 16 0.1 The calculation goes ok, but I do not get the summary table with the respective energies in the output (for each parameter combination, as is provided in the output with the scan keyword). My second question is, when I want to incorporate solvent effects (like the PCM model: #HF/STO-3G opt=z-matrix SCRF(PCM, solvent=chloroform) test) the calculation terminates with an error (using the same z-matriz input file): NAtoms= 16 NActive= 16 NUniq= 16 SFac= 1.00D+00 NAtFMM= 60 Big=F ------------------------------------------------------------------------------ United Atom Topological Model (UA0 parameters set). UA0: Hydrogen 16 is unbound. Keep it explicit at all point on the UA0: potential energy surface to get meaningful results. Error termination via Lnk1e in /software/gaussian/g03_B.4/g03/l301.exe at Wed May 5 00:36:02 2004. Job cpu time: 0 days 0 hours 0 minutes 2.3 seconds. File lengths (MBytes): RWF= 18 Int= 0 D2E= 0 Chk= 1 Scr= 1 Could anybody give me some useful suggestions concerning this problem? Thanks a lot in advance. Carsten -- Carsten Detering University of Washington Seattle, WA 98195 Fon 206.543.5081 Fax 206.685.8665