From owner-chemistry@ccl.net Mon Apr 24 08:21:00 2006 From: "Goedele Roos groos##vub.ac.be" To: CCL Subject: CCL:G: Frequency calculation with fixed atoms. Message-Id: <-31583-060424080338-6645-W/ppubOFzGqCeRMmUc0zQg#server.ccl.net> X-Original-From: Goedele Roos Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1" Date: Mon, 24 Apr 2006 13:09:17 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Goedele Roos [groos(~)vub.ac.be] Hello, This is also of intrest for me... I often optimize with constraints but can I use this frozen geometry for example to calculate the frequencies of an H-bond? best regards, Goedele >Sent to CCL by: "Shobe, David" [dshobe]=[sud-chemieinc.com] >Ramon, > >When you use calcfc, you un-freeze the frozen atoms. So you'll have to freeze them again. Something similar may be happenign with readfc. > >What exactly are you trying to do here? Have you optimized the TS using the constraints (the frozen atoms) and now you want to remove these constraints and re-optimize? Or do you want to keep the previously frozen atoms frozen? > >--David Shobe, Ph.D., M.L.S. >Süd-Chemie, Inc. >phone (502) 634-7409 >fax (502) 634-7724 > >Don't bother flaming me: I'm behind a firewall. > > > >-----Original Message----- >> From: owner-chemistry,,ccl.net [mailto:owner-chemistry,,ccl.net] >Sent: Wednesday, April 19, 2006 12:31 PM >To: Shobe, David >Subject: CCL:G: Frequency calculation with fixed atoms. > >Sent to CCL by: Ramon Crehuet [rcsqtc .. iiqab.csic.es] Dear CCLers, > A few weeks ago I posted a question on how to calculate frequencies when a number of atoms are fixed. I got a solution, but now we have a related problem. > I have used the ONIOM method in Gaussian 03 to optimize a transition state structure keeping several atoms fixed, but I have come up with a problem when reading a hessian. Firstly, I did a frequency calculation on the free atoms, including "-1" on frozen atoms an "0" on free atoms, and I obtained 1 negative eigenvalue: > >/ 1 2 3 > A A A >Frequencies -- -41.1853 54.9227 70.3016 >Red. masses -- 6.2379 7.0722 3.5451 >Frc consts -- 0.0062 0.0126 0.0103 >IR Inten -- 17.8501 1.2021 1.2536 >Atom AN X Y Z X Y Z X Y Z > 1 8 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 >0.00 > 2 6 0.01 -0.02 -0.03 0.00 0.07 0.02 0.19 0.29 >-0.13 > 3 8 0.01 -0.01 -0.05 0.00 0.06 0.03 0.04 0.10 >-0.01/ > > >When I read the hessian from the checkpoint file (using the ReadFC keyword), in order to optimize the TS, I find that apparently the first point of the procedure does not use the previous hessian because now it has 5 negative eigenvalues: > >/Search for a saddle point. >Step number 1 out of a maximum of 696 >All quantities printed in internal units (Hartrees-Bohrs-Radians) Swaping is turned off. >Second derivative matrix not updated -- first step. > Eigenvalues --- -0.00345 -0.00110 -0.00033 -0.00022 -0.00004 > Eigenvalues --- 0.00002 0.00004 0.00016 0.00017 0.00032 > Eigenvalues --- 0.00033 0.00036 0.00041 0.00047 0.00051/ > >In addition, if I calculate the hessian analitically at the first point instead of reading it from a checkpoint file (using the CalcFC keyword) I obtain 4 negative eigenvalues: > >/ >Search for a saddle point. >Step number 1 out of a maximum of 696 >All quantities printed in internal units (Hartrees-Bohrs-Radians) >Swaping is turned off. >Second derivative matrix not updated -- analytic derivatives used. > Eigenvalues --- -0.00053 -0.00020 -0.00014 -0.00002 0.00009 > Eigenvalues --- 0.00016 0.00017 0.00018 0.00025 0.00027 > Eigenvalues --- 0.00036 0.00039 0.00054 0.00066 0.00080/ > > >It is clear that the hessian it reads is different from either the one >> from the checkpoint file or the one it calculates. Why are there these >differences, if they should all be the same? And, how should I carry out >the TS optimization successfully? >Thanks in advance, > >Ramonhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. >Thank you.> > > > Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17