From owner-chemistry@ccl.net Sun Dec 16 20:25:01 2007 From: "Jun Tie Cheng tjcheng^mail.sioc.ac.cn" To: CCL Subject: CCL: Any open-sourced generation algorithm for Connolly molecular surface?? Message-Id: <-35865-071216194457-22847-oZxhrTzQV+8BE9HOYcjBnw^_^server.ccl.net> X-Original-From: "Jun Tie Cheng" Date: Sun, 16 Dec 2007 19:44:52 -0500 Sent to CCL by: "Jun Tie Cheng" [tjcheng**mail.sioc.ac.cn] Hi, CCLers Recently I am dealing with molecular surface generation. Is there any open-sourced alogrithm for this purpose? A C/C++ library would be very appreciated. Thanks in advance. Best regards, Jay From owner-chemistry@ccl.net Sun Dec 16 23:31:00 2007 From: "Jianping Wang jwang*iccas.ac.cn" To: CCL Subject: CCL:G: Overtone Frequency Calculations in Gaussian Message-Id: <-35866-071215232021-29913-QFUlcUN75T8SuYkR43Hxvg[a]server.ccl.net> X-Original-From: "Jianping Wang" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="GB2312" Date: Sun, 16 Dec 2007 03:15:05 GMT Mime-Version: 1.0 Sent to CCL by: "Jianping Wang" [jwang~~iccas.ac.cn] To perform an anharmonic frequency calculation, do this: #P B3lyp/6-31+G* OPT Freq(anharmonic) test To restart a job that is unfinished due to time running out, or for large molecules, do this: #P B3lyp/6-31+G* Freq(anharmonic, restart) IOP(4/5=7) Test geom=allcheck guess=read This surely works. ---------------------------------------------------- Jianping Wang Ph.D., Professor Molecular Reaction Dynamics Laboratory Center for Molecular Science Institute of Chemistry Chinese Academy of Sciences No.2, 1st North Street, Zhongguancun Tel: 86-10-62656806; Fax: 86-10-62563167 Email: jwang . iccas.ac.cn ---------------------------------------------------- Jens Spanget-Larsen spanget(!)ruc.dk Wrote: Sent to CCL by: Jens Spanget-Larsen [spanget[#]ruc.dk] Dear Roman, it is not clear from the information in the enclosed part of your Gaussian printout that the computation has actually stopped. Are you sure that it has really stopped? Calculations with the option freq=anharmonic tend to use an incredidable amount of cpu time, they may seem to last forever and ever and never finish! - I suggest you submit some jobs with very small and medium sized molecules in order to get a feeling for this type of calculation and the required computer times. Yours, Jens >--< -------------------------------------------------- JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget^-^ruc.dk DK-4000 Roskilde, Denmark http://ruc.dk/~spanget -------------------------------------------------- Quoting "Roman D. Gorbunov rgorbuno/aaecom.yu.edu" : Sent to CCL by: "Roman D. Gorbunov" [rgorbuno]=[aecom.yu.edu] Dear CCL Subscribers, I need to calculate overtone anharmonicities with the Gaussian. Trying to do that I have included the following keywords into my input file: #B3LYP/6-31+G(d) GFINPUT IOP(7/33=1) Freq=(HPModes,Anharmonic) And i cannot get the "Normal Termination". The calculations stop with the following message: -------------------------------------------------------------- **** Warning!!: The largest alpha MO coefficient is 0.71988579D+02 Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 17 centers at a time, making 1 passes doing MaxLOS=2. FoFDir/FoFCou used for L=0 through L=2. Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. Store integrals in memory, NReq= 148451441. There are 51 degrees of freedom in the 1st order CPHF. 48 vectors were produced by pass 0. AX will form 48 AO Fock derivatives at one time. 48 vectors were produced by pass 1. -------------------------------------------------------------- It should be mentioned that the problem is related with the "Anharmonic" keyword (since without it I get the "Normal Termination"). Could you pleas help with this problem? Romanhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt