From owner-chemistry@ccl.net Fri Sep 23 02:59:00 2011 From: "ABHISHEK SHAHI shahi.abhishek1984#gmail.com" To: CCL Subject: CCL:G: G09: Convergence Issues for H-Bonded Systems Message-Id: <-45500-110923024857-27034-QTFxv2D0Qumo+vtFwUoKQQ{}server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=0016e6506128898f9604ad9633c0 Date: Fri, 23 Sep 2011 12:18:28 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984*_*gmail.com] --0016e6506128898f9604ad9633c0 Content-Type: text/plain; charset=ISO-8859-1 Dear Sam , Once i solved the problem of negative frequencies by *subtracting or adding * the coordinates of negative frequency (Get it from freq. calculation)* to the* molecular specification coordinates (it should be the final coordinates in which negative frequency exist). If its painful then use matlab or any matrix adding/subtracting program to make the addition or subtraction easy. Hope it may work for you. By doing this we are mainly working against the negative frequency. hopefully you are using the keyword "nosymm" along with all others. Thanks & regards; *ABHISHEK SHAHI* *Research Scholar Inorganic and Physical Chemistry Indian Institute Of Science Bangalore-12* India E-mail: shahi#%#ipc.iisc.ernet.in shahi.abhishek1984#%#gmail.com On Thu, Sep 22, 2011 at 10:59 PM, Arne Dieckmann adieckma^googlemail.com < owner-chemistry#%#ccl.net> wrote: > > Sent to CCL by: Arne Dieckmann [adieckma . googlemail.com] > I would not consider -1.9 wavenumbers an imaginary frequency. Have a look > at the Gaussian manual and whitepapers, there is a section about this issue. > > Cheers, > Arne > > On Sep 22, 2011, at 8:25 AM, Sam Abrash sabrash]_[richmond.edu wrote: > > > > > Sent to CCL by: "Sam Abrash" [sabrash_+_richmond.edu] > > Hi Folks, > > > > I have a job involving hydrogen bonding of 3 acetylenes to the benzene > cation. I'm having trouble with the geometric convergence. I was able to > get the system to converge with normal convergence criteria, opt=calcall, > and MaxStep=5, but then I got an imaginary frequency of -1.9 wavenumbers. > > > > Subsequently, I changed to Opt=tight, tried both calcfc and calcall, and > have steadily reduced MaxStep to 1, but it still won't converge. The force > constant criteria have been met, but the problem is the displacement > criteria. Both this observation and looking at the structures with JMOL > show that the problem is finding the minimum in a very shallow potential. > > > > Two questions. First, is the 1.9 wavenumber imaginary frequency real or > an artifact? Second, any advice on how to force the system to converge? > Model chemistry is M062X/6-311++G**. > > > > Thanks! > > Sam> > > --0016e6506128898f9604ad9633c0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sam ,

=A0Once i solved the problem of negative frequencies by = subtracting or adding the coordinates of negative frequency (Get it = > from freq. calculation) to the molecular specification coordinates (= it should be the final coordinates in which negative frequency exist). If i= ts painful then use matlab or any matrix adding/subtracting program to make= the addition or subtraction easy. Hope it may work for you. By doing this = we are mainly working against the negative frequency. hopefully you are usi= ng the keyword "nosymm" along with all others.=A0




Thanks & = regards;
=A0<= font style=3D"font-family:trebuchet ms,sans-serif" size=3D"4">ABHISHEK SHAHI

Research ScholarInorganic= and Physical Chemistry
In= dian Institute Of Science
Bangalore-12
India
E-mail: =A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 shahi#%#ipc.iisc.ernet.in
=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 shahi.abhishek1984#%#gmail.com




On Thu, Sep 22, 2011 at 10:59 PM, Arne D= ieckmann adieckma^googlemail.com <owner-chemistr= y#%#ccl.net> wrote:

Sent to CCL by: Arne Dieckmann [adieckma . googlemail.com]
I would not consider -1.9 wavenumbers an imaginary frequency. Have a look a= t the Gaussian manual and whitepapers, there is a section about this issue.=

Cheers,
Arne

On Sep 22, 2011, at 8:25 AM, Sam Abrash sabrash]_[richmond.edu wrote:

>
> Sent to CCL by: "Sam =A0 Abrash" [sabrash_+_richmond.edu]
> Hi Folks,
>
> I have a job involving hydrogen bonding of 3 acetylenes to the benzene= cation. =A0I'm having trouble with the geometric convergence. =A0I was= able to get the system to converge with normal convergence criteria, opt= =3Dcalcall, and MaxStep=3D5, but then I got an imaginary frequency of -1.9 = wavenumbers.
>
> Subsequently, I changed to Opt=3Dtight, tried both calcfc and calcall,= and have steadily reduced MaxStep to 1, but it still won't converge. = =A0The force constant criteria have been met, but the problem is the displa= cement criteria. =A0Both this observation and looking at the structures wit= h JMOL show that the problem is finding the minimum in a very shallow poten= tial.
>
> Two questions. =A0First, is the 1.9 wavenumber imaginary frequency rea= l or an artifact? =A0Second, any advice on how to force the system to conve= rge? =A0Model chemistry is M062X/6-311++G**.
>
> Thanks!
> Sam>
>



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--0016e6506128898f9604ad9633c0-- From owner-chemistry@ccl.net Fri Sep 23 04:02:01 2011 From: "Soren Eustis soreneustis!A!gmail.com" To: CCL Subject: CCL:G: G09: Convergence Issues for H-Bonded Systems Message-Id: <-45501-110923040055-10726-vHw37uiVNlpHiuGnaViDIA/a\server.ccl.net> X-Original-From: Soren Eustis Content-Transfer-Encoding: 8bit Content-type: text/plain; charset="ISO-8859-1" Date: Fri, 23 Sep 2011 10:00:37 +0200 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis\a/gmail.com] Sam, It looks like you are taking some good steps to solve this issue. Firstly, the -1.9 wavenumber frequency should not be taken as an indication of a saddle point. The energy is simply too low. Look at the whitepapers on the Gaussian site if in doubt. Your second question would then be negated by my answer to your first question, as it seems you have a valid converged geometry (opt-calcall, maxstep=5). If you were to continue to try the second method with opt=tight, you should use int=ultrafine. This is always a good idea for shallow potential wells and is recommended anytime opt=tight is used. Best, Soren Soren N. Eustis, Ph.D. ETH ­ Zürich Environmental Chemistry Group Institute for Biogeochemistry and Pollutant Dynamics Universitätstrasse 16 CHN F33 8092 ZürichSWITZERLAND +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren a env.ethz.ch On 9/22/11 17:25 , "Sam Abrash sabrash]_[richmond.edu" wrote: > >Sent to CCL by: "Sam Abrash" [sabrash_+_richmond.edu] >Hi Folks, > >I have a job involving hydrogen bonding of 3 acetylenes to the benzene >cation. I'm having trouble with the geometric convergence. I was able >to get the system to converge with normal convergence criteria, >opt=calcall, and MaxStep=5, but then I got an imaginary frequency of -1.9 >wavenumbers. > >Subsequently, I changed to Opt=tight, tried both calcfc and calcall, and >have steadily reduced MaxStep to 1, but it still won't converge. The >force constant criteria have been met, but the problem is the >displacement criteria. Both this observation and looking at the >structures with JMOL show that the problem is finding the minimum in a >very shallow potential. > >Two questions. First, is the 1.9 wavenumber imaginary frequency real or >an artifact? Second, any advice on how to force the system to converge? >Model chemistry is M062X/6-311++G**. > >Thanks! >Sam> > From owner-chemistry@ccl.net Fri Sep 23 05:10:01 2011 From: "Julianna Olah olahjulcsi-x-freemail.hu" To: CCL Subject: CCL:G: close to zero frequencies in Gaussian Message-Id: <-45502-110923044654-16626-uQQQypgINDId3jiHpJLVUw\a/server.ccl.net> X-Original-From: "Julianna Olah" Date: Fri, 23 Sep 2011 04:46:50 -0400 Sent to CCL by: "Julianna Olah" [olahjulcsi.=-=.freemail.hu] Dear CCl subsribers, In his yesterdays's letter arne suggested (see below) that he would not consider -1.9 wavenumber a negative freuency and to read the corresponding gaussian white paper on it. I did it and looked at one of my calculations (which I knew had a similar problem, it is a TS state optimization of a heme-oxo compound with B3LYP) I found the following: --from gaussian output--- Full mass-weighted force constant matrix: Low frequencies --- -304.9594 -11.0064 -4.7744 0.0008 0.0013 0.0016 Low frequencies --- 8.1799 10.3059 40.8254 ****** 2 imaginary frequencies (negative Signs) ****** Diagonal vibrational polarizability: 200.5107265 1512.4391110 75.5726076 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), depolarization ratios for plane and unpolarized incident light, reduced masses (AMU), force constants (mDyne/A), and normal coordinates: 1 2 3 A A A Frequencies -- -304.9584 -1.0021 40.8073 Red. masses -- 10.8546 5.6718 5.5273 Frc consts -- 0.5948 0.0000 0.0054 IR Inten -- 140.3088 0.0608 0.0351 --- end of gaussian output--- I would like to as the following: 1. Do you know why when frequencies listed as low and when they are listed in more detail are not exactly the same? 2. I see the three almost equal to zero frequencies,and understand they belong to translations, but from the low frequencies line how would I know which frequencies belong to rotations? 3. The way how gaussian calculated frequencies ensures with 100% certainty that rotations are properly selected? (e.g. in this case might it not have happened that the -1.0021 frequency belong to a rotation? ) (well when I visualize it it does not look like rotation of the molecules, in any case, but I tried optimizing the TS from several initial structures and I always get back this -1 frequency) 4. do I need to worry about this? I would think this would not influence seriously the energy of the TS, but what is your opinion? Thank you very much in advance, cheers, Julianna On Thu, Sep 22, 2011 at 10:59 PM, Arne Dieckmann adieckma^googlemail.com wrote: Sent to CCL by: Arne Dieckmann [adieckma . googlemail.com] I would not consider -1.9 wavenumbers an imaginary frequency. Have a look at the Gaussian manual and whitepapers, there is a section about this issue. Cheers, Arne From owner-chemistry@ccl.net Fri Sep 23 11:07:00 2011 From: "Masoud Nahali m_nahali ~ alum.sharif.edu" To: CCL Subject: CCL: Fractional to orthonormal converting matrix Message-Id: <-45503-110923105102-31264-9ABQuv/af3w5XdvU09IQjw^server.ccl.net> X-Original-From: "Masoud Nahali" Date: Fri, 23 Sep 2011 10:50:59 -0400 Sent to CCL by: "Masoud Nahali" [m_nahali=alum.sharif.edu] Dear CCL Friends There is a matrix that converts fractional coordinates to orthonormal ones and certainly the vice versa could be done by an inverted matrix. In the following link you can find this matrix and a brief justification. http://www.angelfire.com/linux/myp/FracCor/fraccor.html There are 2 limitations in this approach since we have to take one of the vectors on X axis and also another vector must be on X-Y plane. I need a general form of such converting matrix without the 2 limitations. I mean that a, b, and c vectors shouldn't be limited to locate in/on a specific direction (plane) like X-axis or X-Y plane. I appreciate any suggestion in advance to find it. Best Wishes Masoud From owner-chemistry@ccl.net Fri Sep 23 11:57:00 2011 From: "Herbert Fruchtl herbert.fruchtl..st-andrews.ac.uk" To: CCL Subject: CCL: Fractional to orthonormal converting matrix Message-Id: <-45504-110923115509-24582-B33sNrGTfufTiJ0DO+K2SQ^server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 Sep 2011 16:54:21 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl::st-andrews.ac.uk] Fractional coordinates, in connection with lattice parameters (lengths and angles rather than lattice vectors), don't contain any information about orientation in a Cartesian coordinate system, so you have to choose one. If you multiply the transformation matrix described in your link with a rotation matrix (rotating your coordinates around any axis by any angle), you get another valid transformation matrix. You don't say which orientation you want instead of the simplest one. HTH, Herbert On 23/09/11 15:50, Masoud Nahali m_nahali ~ alum.sharif.edu wrote: > > Sent to CCL by: "Masoud Nahali" [m_nahali=alum.sharif.edu] > Dear CCL Friends > > There is a matrix that converts fractional coordinates to orthonormal ones and certainly the vice versa could be done by an inverted matrix. In the following link you can find this matrix and a brief justification. > > http://www.angelfire.com/linux/myp/FracCor/fraccor.html > > There are 2 limitations in this approach since we have to take one of the vectors on X axis and also another vector must be on X-Y plane. > > I need a general form of such converting matrix without the 2 limitations. I mean that a, b, and c vectors shouldn't be limited to locate in/on a specific direction (plane) like X-axis or X-Y plane. I appreciate any suggestion in advance to find it. > > > > Best Wishes > Masoud> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Fri Sep 23 13:30:00 2011 From: "Arne Dieckmann adieckma]^[googlemail.com" To: CCL Subject: CCL:G: close to zero frequencies in Gaussian Message-Id: <-45505-110923132801-25560-Qi57K9xbAC+fi1kKRkRLfw:+:server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 23 Sep 2011 10:27:52 -0700 Mime-Version: 1.0 (Apple Message framework v1244.3) Sent to CCL by: Arne Dieckmann [adieckma*googlemail.com] -304 is definately a true imaginary frequency, while -1.9 or 1.0 can be considered to be zero. Again, the Gaussian whitepapers contain information about as when to regard a frequency as imaginary. Arne On Sep 23, 2011, at 1:46 AM, Julianna Olah olahjulcsi-x-freemail.hu wrote: > > Sent to CCL by: "Julianna Olah" [olahjulcsi.,,.freemail.hu] > Dear CCl subsribers, > > In his yesterdays's letter arne suggested (see below) that he would not consider -1.9 wavenumber a negative freuency and to read the corresponding gaussian white paper on it. > I did it and looked at one of my calculations (which I knew had a similar problem, it is a TS state optimization of a heme-oxo compound with B3LYP) > > I found the following: > > --from gaussian output--- > Full mass-weighted force constant matrix: > Low frequencies --- -304.9594 -11.0064 -4.7744 0.0008 0.0013 0.0016 > Low frequencies --- 8.1799 10.3059 40.8254 > ****** 2 imaginary frequencies (negative Signs) ****** > Diagonal vibrational polarizability: > 200.5107265 1512.4391110 75.5726076 > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering > activities (A**4/AMU), depolarization ratios for plane and unpolarized > incident light, reduced masses (AMU), force constants (mDyne/A), > and normal coordinates: > 1 2 3 > A A A > Frequencies -- -304.9584 -1.0021 40.8073 > Red. masses -- 10.8546 5.6718 5.5273 > Frc consts -- 0.5948 0.0000 0.0054 > IR Inten -- 140.3088 0.0608 0.0351 > > --- end of gaussian output--- > > I would like to as the following: > > 1. Do you know why when frequencies listed as low and when they are listed in more detail are not exactly the same? > > 2. I see the three almost equal to zero frequencies,and understand they belong to translations, but from the low frequencies line how would I know which frequencies belong to rotations? > > 3. The way how gaussian calculated frequencies ensures with 100% certainty that rotations are properly selected? (e.g. in this case might it not have happened that the -1.0021 frequency belong to a rotation? ) (well when I visualize it it does not look like rotation of the molecules, in any case, but I tried optimizing the TS from several initial structures and I always get back this -1 frequency) > > 4. do I need to worry about this? I would think this would not influence seriously the energy of the TS, but what is your opinion? > > Thank you very much in advance, > cheers, > Julianna > > > > On Thu, Sep 22, 2011 at 10:59 PM, Arne Dieckmann adieckma^googlemail.com wrote: > > > Sent to CCL by: Arne Dieckmann [adieckma . googlemail.com] > I would not consider -1.9 wavenumbers an imaginary frequency. Have a look at the Gaussian manual and whitepapers, there is a section about this issue. > > Cheers, > Arne> > From owner-chemistry@ccl.net Fri Sep 23 23:59:00 2011 From: "Sandhya Rai sandhyachemistry30*o*gmail.com" To: CCL Subject: CCL: High virial ratio Message-Id: <-45506-110923235722-7196-Za+0oVTdWcTMzS+24mRiGw]![server.ccl.net> X-Original-From: "Sandhya Rai" Date: Fri, 23 Sep 2011 23:57:19 -0400 Sent to CCL by: "Sandhya Rai" [sandhyachemistry30,gmail.com] Dear all, I am studying metal interactions with biomolecules. Some times I get very high virial ratio like 4.09 etc. The frequency values are all real and the output structures are also fine. Can any one suggest me what might be going wrong. The metal I use is gold Thanks in advance! Sandhya Rai Pursuing Ph.D IIIT hyderabad