From chemistry-request@ccl.net Tue Feb 17 11:56:08 2004 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1HGu5Df009162 for ; Tue, 17 Feb 2004 11:56:06 -0500 Received: by CELEBRIS04 with Internet Mail Service (5.5.2653.19) id <10JDFXYF>; Tue, 17 Feb 2004 13:56:23 -0300 Message-ID: <9E7055859B0BD811AE7B00105AD16BDF69A916@CELEBRIS04> From: Pedro Aprigliano Fernandes To: "'chemistry)at(ccl.net'" Subject: CCL: minimum geometry and imaginary frequencies Date: Tue, 17 Feb 2004 13:56:16 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain X-Spam-Status: No, hits=0.0 required=7.0 tests=none 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 CCLers, I am trying to optimize and calculate the minimum geometry of a molecule in gaussian 98. How do I know that i have found that geometry in optimization and where do i search in the output file for imaginary frequencies? I have included here a cutout of my output wich shows negative low frequencies, but this is really a imaginary frequency? I am not a member of the CCL so please reply directly to my e-mail: pfernandes)at(cetem.gov.br N-N= 3.997713045864D+02 E-N=-1.603506616097D+03 KE= 3.445396433384D+02 Exact polarizability: 89.458 -0.107 39.829 -0.064 6.606 119.415 Approx polarizability: 150.116 -0.187 50.980 -0.029 2.556 165.619 Full mass-weighted force constant matrix: Low frequencies --- -8.0171 -0.0006 0.0004 0.0005 11.6757 12.6686 Low frequencies --- 49.6615 95.7842 104.8786 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 ?A ?A ?A Frequencies -- 49.5388 95.7622 104.8667 Red. masses -- 2.5902 1.9409 3.9429 Frc consts -- 0.0037 0.0105 0.0255 IR Inten -- 0.0139 0.0012 0.4366 Raman Activ -- 0.0000 0.0000 0.0000 Depolar -- 0.0000 0.0000 0.0000 Atom AN X Y Z X Y Z X Y Z 1 6 -0.01 0.11 0.06 0.03 0.00 -0.04 0.00 0.09 0.06 2 6 0.06 0.11 0.06 -0.02 0.00 -0.04 0.00 -0.12 0.05 3 6 0.09 0.00 0.00 -0.04 0.00 0.00 0.00 -0.20 0.04 From chemistry-request@ccl.net Mon Feb 16 21:59:36 2004 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1H2xS3T001204 for ; Mon, 16 Feb 2004 21:59:30 -0500 Received: from mail.ustc.edu.cn (webmail.ustc.edu.cn [202.38.64.16]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with SMTP id KAA00518 for ; Tue, 17 Feb 2004 10:58:43 +0800 Received: from 202.38.82.52 (SquirrelMail authenticated user hzhan) by webmail.ustc.edu.cn with HTTP; Tue, 17 Feb 2004 10:51:07 +0800 (CST) Message-ID: <1150.202.38.82.52.1076986267.squirrel.-at-.webmail.ustc.edu.cn> Date: Tue, 17 Feb 2004 10:51:07 +0800 (CST) Subject: Where can I find the source code of GCMC? From: "Zhan Huan" To: chemistry.-at-.ccl.net Reply-To: hzhan.-at-.mail.ustc.edu.cn X-Mailer: SquirrelMail (version 1.3.2) MIME-Version: 1.0 Content-Type: text/plain;charset=gb2312 X-Priority: 3 Importance: Normal X-Spam-Status: No, hits=0.1 required=7.0 tests=RCVD_IN_RFCI 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! These days I want to do some molecule simulations with GCMC (grand canonical Monte Carlo) method. Is there anyone that can tell me where I can download the source code of GCMC and thank you! From chemistry-request@ccl.net Tue Feb 17 14:01:03 2004 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1HJ10Df011904 for ; Tue, 17 Feb 2004 14:01:01 -0500 Received: by CELEBRIS04 with Internet Mail Service (5.5.2653.19) id <10JDFYG8>; Tue, 17 Feb 2004 16:01:21 -0300 Message-ID: <9E7055859B0BD811AE7B00105AD16BDF69A918@CELEBRIS04> From: Pedro Aprigliano Fernandes To: "'Chemistry.-at-.ccl.net'" Subject: CCL: Summary minimum geometry and imaginary frequencies Date: Tue, 17 Feb 2004 16:01:20 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none 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 CCLers, I am trying to optimize and calculate the minimum geometry of a molecule in gaussian 98. How do I know that i have found that geometry in optimization and where do i search in the output file for imaginary frequencies? I have included here a cutout of my output wich shows negative low frequencies, but this is really a imaginary frequency? I am not a member of the CCL so please reply directly to my e-mail: pfernandes.-at-.cetem.gov.br N-N= 3.997713045864D+02 E-N=-1.603506616097D+03 KE= 3.445396433384D+02 Exact polarizability: 89.458 -0.107 39.829 -0.064 6.606 119.415 Approx polarizability: 150.116 -0.187 50.980 -0.029 2.556 165.619 Full mass-weighted force constant matrix: Low frequencies --- -8.0171 -0.0006 0.0004 0.0005 11.6757 12.6686 Low frequencies --- 49.6615 95.7842 104.8786 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 ?A ?A ?A Frequencies -- 49.5388 95.7622 104.8667 Red. masses -- 2.5902 1.9409 3.9429 Frc consts -- 0.0037 0.0105 0.0255 IR Inten -- 0.0139 0.0012 0.4366 Raman Activ -- 0.0000 0.0000 0.0000 Depolar -- 0.0000 0.0000 0.0000 Atom AN X Y Z X Y Z X Y Z 1 6 -0.01 0.11 0.06 0.03 0.00 -0.04 0.00 0.09 0.06 2 6 0.06 0.11 0.06 -0.02 0.00 -0.04 0.00 -0.12 0.05 3 6 0.09 0.00 0.00 -0.04 0.00 0.00 0.00 -0.20 0.04 Here are the answers i received: ----------------------------------------------------------------------- I think you are done. Starting with the first entry marked 1 ?A 49.5388 you have a positive value. SO this means that you have "no negative frequencies" in you table. The negative ones are listed first. If you were trying to optimize to a transition state, you would look for one negative frequency here. But just for an OPT run, this looks fine to me. ------------------------------------------------------------------------ That looks like a good clean minimum. Youve found the right place to look at frequencies and the one negative low frequency that youv'e found is not of concern. In genreal an negative frequency below 45cm-1 is ok or if using DFT perhaps 60cm-1. To know that an optimization job has completed normaly look for a a section like this Maximum Force 0.000250 0.000450 YES RMS Force 0.000221 0.000300 YES Maximum Displacement 0.000519 0.001800 YES RMS Displacement 0.000463 0.001200 YES Predicted change in Energy=-2.225553D-07 Optimization completed. -- Stationary point found. Alternatly you will probably fing the word GINC in the file. Most sucesfull optimiztions will give you a quote at the end but this doesn't always indicate a sucesfull completion. ----------------------------------------------------------------------- Hi! You are looking at the right place, but what you`ve got is not a transition state, it is some local or global minimum. For a TS, you should have a large negative number for the first frequency (instead of 49.5 cm-) here > 1 2 3 > ?A ?A ?A > Frequencies -- 49.5388 95.7622 104.8667 By the way, you should have one and only one negative frequency. More than one (-) frequencies means this is a higher order saddle point, not a real transition state. The following numbers, I believe, correspond to the 6 non-vibrational degrees of freedom (3 for rotation + 3 for translation): > Low frequencies --- -8.0171 -0.0006 0.0004 0.0005 11.6757 > 12.6686 Ideally these should be zero of course, and they actually are pretty close to zero. Finally, even if you get 1 imaginary frequency, you should always check the motion of the atoms to make sure that it makes sense. That is, you may have ended up with a different TS than the one you want. ------------------------------------------------------------------------- The first six low frequencies in the gaussian output (you will see that they are separated from the "other" low frequencies), correspond to the translation and rotation of the molecule as a whole, and they should ideally be zero. If you are looking for a transition state you need an imaginary frequency that corresponds to a normal vibrational mode. Once you have located a stationary point with one negative frequency, it is often useful to "animate" the vibrational modes (you can do it with a program like "molden") to check if the movement corresponds to the one you are looking for. For what I read in the output file you have sent, I would say that you have just located a minimum. ------------------------------------------------------------------------ It is my understanding that the low frequencies listed are rotational frequencies that can be ignored. The first "real" frequency would be the one labeled as "1", i.e., 49.5388. -------------------------------------------------------------------------