From owner-chemistry@ccl.net Tue Aug 14 12:26:00 2007 From: "William Wei william.wei!^!utoronto.ca" To: CCL Subject: CCL:G: Freezing tortinal angle in Gaussian98 Message-Id: <-34924-070814121644-15409-2Z2evf40bvRHciCvbCNepA[#]server.ccl.net> X-Original-From: "William Wei" Date: Tue, 14 Aug 2007 12:16:39 -0400 Sent to CCL by: "William Wei" [william.wei+*+utoronto.ca] Hi friends, I am trying to do a PES scan in Gaussian. The starting structure is a chemistry unfavorable geometry. The conformation is from protein binding site. The structure is an substituted pyrimidine ring. Atom bond to pyrimidine rine is out of the pyrimidine ring about 30 degree. During the calculation, I want to freeze the tortional angle to the starting point. But as optimization going, the torsional angle changed and the atom I frozen was come back to the plane of pyrimidine ring. Here is several tries of my gaussian PES scan input: 1: B3LYP/6-31G SCF(QC,MaxCycle=1000) SCF=Tight Opt=Z-matrix geometry optimization in Gas phase 0,1 C1 C2 1 B1 C3 2 B2 1 A1 C4 3 B3 2 A2 1 D1 C5 4 B4 3 A3 2 D2 ..... Variables: B1 2.47926824 B2 2.48671691 B3 1.43000350 B4 1.37717101 A7 153.89667949 S 4 -10.0 .... Constants: A4 111.91158489 D3 153.66578065 D6 -83.27112538 those constants was changed as calculation going. 2: %Chk=6CN_DFT631_ZMat2_C6O_Scan.chk B3LYP/6-31G Opt=ModRedundant geometry optimization in Gas phase 0,1 C1 C2 1 B1 C3 2 B2 1 A1 C4 3 B3 2 A2 1 D1 C5 4 B4 3 A3 2 D2 ...... Variables: B1 2.47926824 B2 2.48671691 B3 1.43000350 B4 1.37717101 B11 3.46203 S 5 -0.5 A4 111.91158489 S 0 0.0 D3 153.66578065 S 0 0.0 A7 153.89667949 S 0 0.0 D6 -83.27112538 S 0 0.0 .... A 7 5 18=108.00687 F 103.0 113.0 instead of using constants, I set 0 step scan for those angles I want to freeze. 3: B3LYP/6-31G SCF(QC,MaxCycle=1000) SCF=Tight Opt=ModRedundant geometry optimization in Gas phase 0,1 C1 0.8561 -0.7978 -11.7910 C2 3.2151 -0.1768 -12.2340 C3 5.0361 -1.2548 -10.9280 C4 4.0591 -2.0648 -10.2690 C5 2.7191 -1.9348 -10.5590 C6 1.9791 -3.1758 -10.2980 ...... A 6 5 4=111.91158 F D 6 5 4 3=153.66578 F A 9 6 5=153.89668 F D 9 6 5 4=-83.27113 F A 7 5 18=108.00687 F B 5 12 =3.46203 S 5 0.5 Instead of Z-Matrix, I use cartesian coordinates system. All of these input do not freeze the angles. Could anyone give me help? I appriciate it. Have a good day, William From owner-chemistry@ccl.net Tue Aug 14 13:02:01 2007 From: "Wolfram Altenhofen wolfram|-|chemcomp.com" To: CCL Subject: CCL: European User Group Meeting 2007 Message-Id: <-34925-070814115653-12450-+lF2LP0yYsqgWnez8hTc8Q,,server.ccl.net> X-Original-From: "Wolfram Altenhofen" Date: Tue, 14 Aug 2007 11:56:49 -0400 Sent to CCL by: "Wolfram Altenhofen" [wolfram],[chemcomp.com] October 8-11, 2007 Berlin, Germany Chemical Computing Group is pleased to announce the annual European User Group Meeting. The two-day meeting will include talks and software demonstrations by MOE users describing research projects utilizing the MOE software. CCG staff will present recent developments and future directions in MOE. Following the meeting there will be options for training sessions on Oct 10th and 11th. CCG invites MOE users to present either a talk, software demonstration, or a poster of their research, and how MOE is used to advance their work. Proposals can be submitted using the online Talk & Poster form (http://www.chemcomp.com/ugm-euro2007-submit.htm). More information on the meeting and accommodation details as well as a form for registration can be found on (http://www.chemcomp.com/ugm-euro2007.htm). To speak with someone directly please contact Dr. Wolfram Altenhofen at: +49 221 97761290. Dr. Wolfram Altenhofen Director of Scientific Services Chemical Computing Group AG Kaiser-Wilhelm-Ring 11 50672 Kln Germany From owner-chemistry@ccl.net Tue Aug 14 13:37:00 2007 From: "Tanguy Van Regemorter tanguy.vr . yucom.be" To: CCL Subject: CCL:G: Surface chemistry with a cluster model: Good references ? Message-Id: <-34926-070814111346-5882-u512Y/WY8aiW/DAwk9eLrg*server.ccl.net> X-Original-From: "Tanguy Van Regemorter" Date: Tue, 14 Aug 2007 11:13:41 -0400 Sent to CCL by: "Tanguy Van Regemorter" [tanguy.vr * yucom.be] Hello everybody, I am PhD student and I am working on the modelling of the chemistry at the diamond surface during the growth by chemical vapour deposition. Until now, I have perform plane wave calculations (Using the program CASTEP) but I would like to perform some cluster calculations using Gaussian. I have build different model size for the two surface orientations I am interested in (111 and 100). For the different size, I have calculated the CH3 adsorption energy in order to quantify the size effect. > From these calculation, I obtained different values for the adsorption energy but I have some problem to analyse them correctly. I tend to compare them to the values I have obtained with my plane-wave calculations but I am not sure that it is a correct way to proceed. Since this type of calculations are rather new for me, I have been looking for references or books which could help me but I seems to be rather tricky. Is there anybody who could give me some advices or good reference on this type of calculations (i.e. comparison between plane-wave and cluster calculations for surface reactivity) even if it is for different materials ? Thank you very much in advance ! Best Regards, Tanguy Van Regemorter From owner-chemistry@ccl.net Tue Aug 14 22:06:01 2007 From: "Jingtao Lu tower.lu^gmail.com" To: CCL Subject: CCL:G: help on Gaussian error: bad length for file Message-Id: <-34927-070814215256-14517-pxddVOXg1jmtpLm7AUlJ8w~!~server.ccl.net> X-Original-From: "Jingtao Lu" Date: Tue, 14 Aug 2007 21:52:51 -0400 Sent to CCL by: "Jingtao Lu" [tower.lu * gmail.com] hi, I am running a frequency job using the optimized structure of two carbon nanotube segment with benzene between them. I use freq=anharmonic to get the 3rd and 4th order force constant. I got the following error: Leave Link 703 at Tue Aug 14 23:35:06 2007, MaxMem= 6291456 cpu: 1538.9 (Enter /home/phyljt/gaussian/g03/l716.exe) Dipole =-2.33537862D-01 2.94316513D-01 7.14121565D-01 Polarizability= 5.41394036D+02 1.31151484D+00 2.88361167D+02 4.01627610D-01 4.72214518D-01 2.35279312D+02 HyperPolar =-1.81094944D+02 3.67827384D+02-3.78445671D+00 2.67635817D+02-2.27527010D+02-1.96834912D+00 -1.05325523D+02-6.75776966D+00 1.74318452D+01 -2.81543687D+01 ---------------------------------------------------------------------- Bad length for file. FileIO: IOper= 0 IFilNo(1)= 719 Len= -61266523 IPos= 0 Q= -16640 dumping /fiocom/, unit = 1 NFiles = 81 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 157843968 FType=2 FMxFil=10000 Number 0 0 0 0 0 0 0 0 Base 1645050 1645568 1569792 2261636 1612288 2547712 1617920 1017856 End 1645056 1651712 1570304 2263040 1613824 6391808 1618944 1018880 End1 1645056 1651712 1570304 2263040 1613824 6391808 1618944 1018880 Wr Pntr 1645050 1645568 1569792 2261636 1612288 2547712 1617920 1017856 Rd Pntr 1645050 1645568 1569792 2261636 1612288 2547712 1617920 1017856 Length 6 6144 512 1404 1536 3844096 1024 1024 ... It seems that it is a fileIO error. I tried using several rwf with smaller size. It also didn't work. The disk space is also enough. Any suggestions? Thanks. From owner-chemistry@ccl.net Tue Aug 14 23:27:01 2007 From: "Kaci Tizi_Ouzou kaci.tiziouzou##gmail.com" To: CCL Subject: CCL: Confusion about transition state Message-Id: <-34928-070813125812-30842-jbP6fTte9h0bTMdhUivkUQ(a)server.ccl.net> X-Original-From: "Kaci Tizi_Ouzou" Content-Type: multipart/alternative; boundary="----=_Part_208526_29746886.1187020968490" Date: Mon, 13 Aug 2007 10:02:48 -0600 MIME-Version: 1.0 Sent to CCL by: "Kaci Tizi_Ouzou" [kaci.tiziouzou : gmail.com] ------=_Part_208526_29746886.1187020968490 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all, I think I am getting confused about the transition state calculation. I always believed that a single negative frequency is a sufficient condition for a TS. But I just noticed during a manual PES scan that I had ONE negative frequency before reching the highest energy. Shall I conclude that: A negative frequency is a necessary BUT NOT a sufficient condition for a TS? Cheers Kass ------=_Part_208526_29746886.1187020968490 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi all,
 
I think I am getting confused about the transition state calculation.
 
 
I always believed that a single negative frequency is a sufficient condition for a TS. But I just noticed during a manual PES scan that I had ONE negative frequency before reching the highest energy.
 
Shall I conclude that: A negative frequency is a necessary BUT NOT a sufficient condition for a TS?
 
 
Cheers
 
 
Kass
 
 
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