From owner-chemistry@ccl.net Mon Dec 15 13:00:00 2014 From: "Igors Mihailovs igors.mihailovs0-x-gmail.com" To: CCL Subject: CCL:G: Frequencies from Gaussian 09 Message-Id: <-50819-141215125801-26137-cISwCrpdtj1+sFWQsg6kXg**server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=001a11c3da2e5a90d5050a44fb42 Date: Mon, 15 Dec 2014 19:57:34 +0200 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0---gmail.com] --001a11c3da2e5a90d5050a44fb42 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Dr. Davies, According to Gaussian manual and their book "Exploring chemistry with electronic structure methods", "Low frequencies" list is *not* the actual place where You should look for vibration modes. Probably You would better check table of frequency modes which is below the "Low frequencies" list (starting with "Frequencies --") =E2=80=93 I am pretty sure that first valu= es mentioned there meet well those in WebMO output. For me, I did not ever considered what actually is printed in the "Low frequencies" section, but, thank You, I see now these could be translational/rotational modes. With best wishes, Igors Mihailovs (engineer) Institute of Solid State Physics University of Latvia 2014-12-11 17:51 GMT+02:00 Andrew Davies r.a.davies^-^bangor.ac.uk < owner-chemistry~!~ccl.net>: > > > Sent to CCL by: "Andrew Davies" [r.a.davies*bangor.ac.uk] > During a recent Gaussian 09 run, we obtain the following low frequencies: > -7.3819 -6.1950 -3.9324 -0.0001 0.0007 0.0007 8.7154 19.6298 20.9237 > > When we analyse them using WebMO, it tells us that we have a 1st order TS > where the 1st imaginary (negative) frequency is -6.1950 cm-1. > > I understand that it has to choose 3 vibrational and 3 rotational modes > > from the low frequencies list. Is there a reason why the programs "get > rid > of" specific frequencies. In this example, we lose the 1st, 3rd, 4th, 5th > and 6th modes. Why can't we keep the the first two (giving a 2nd order TS= ) > and get rid of the next six? > > Regards, > > Dr. Andrew Davies > School of Chemistry > Bangor University > UK > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a11c3da2e5a90d5050a44fb42 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Dr. Davies,

According to Gauss= ian manual and their book "Exploring chemistry with electronic structu= re methods", "Low frequencies" list is not the actual= place where You should look for vibration modes. Probably You would better= check table of frequency modes which is below the "Low frequencies&qu= ot; list (starting with "Frequencies --") =E2=80=93 I am pretty s= ure that first values mentioned there meet well those in WebMO output.
<= /div>For me, I did not ever considered what actually is printed in the &quo= t;Low frequencies" section, but, thank You, I see now these could be t= ranslational/rotational modes.

With best wishes,<= br>
Igors Mihailovs (engineer)
Institute of Solid State P= hysics
University of Latvia


2014-12-11 17:51 GMT+02:00 Andrew Davies r.a= .davies^-^bangor.ac.uk <owner-ch= emistry~!~ccl.net>:

Sent to CCL by: "Andrew=C2=A0 Davies" [r.a.davies*bangor.ac.uk]
During a recent Gaussian 09 run, we obtain the following low frequencies: -7.3819 -6.1950 -3.9324 -0.0001 0.0007 0.0007 8.7154 19.6298 20.9237

When we analyse them using WebMO, it tells us that we have a 1st order TS where the 1st imaginary (negative) frequency is -6.1950 cm-1.

I understand that it has to choose 3 vibrational and 3 rotational modes
> from the low frequencies list. Is there a reason why the programs &quo= t;get rid
of" specific frequencies. In this example, we lose the 1st, 3rd, 4th, = 5th
and 6th modes. Why can't we keep the the first two (giving a 2nd order = TS)
and get rid of the next six?

Regards,

Dr. Andrew Davies
School of Chemistry
Bangor University
UK



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--001a11c3da2e5a90d5050a44fb42-- From owner-chemistry@ccl.net Mon Dec 15 15:04:01 2014 From: "Brian Skinn bskinn++alum.mit.edu" To: CCL Subject: CCL:G: Frequencies from Gaussian 09 Message-Id: <-50820-141215150211-28872-l3uboShVAE6LovG7GaxeLw|,|server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=047d7bb709ce3750be050a46b737 Date: Mon, 15 Dec 2014 15:01:41 -0500 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [bskinn+*+alum.mit.edu] --047d7bb709ce3750be050a46b737 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dr. Davies, The projection of translational and rotational character out of the normal modes is a well-defined procedure, and not an arbitrary selection of frequencies to retain/discard. Please see this link on Gaussian's website for more details about what is done: http://www.gaussian.com/g_whitepap/vib.htm. The retention of the identical value of the imaginary frequency after projection (-6.195 cm**-1 both before and after) is probably a numerical quirk of your system. In general, I would expect the value to change at least somewhat after projection. Also, with that small an imaginary frequency, you probably are looking at an imperfectly optimized system with a very flat PES along one or more normal modes. Do you perchance have a methyl group or three in there, prone to internal rotation? Best regards, Brian On Mon, Dec 15, 2014 at 12:57 PM, Igors Mihailovs igors.mihailovs0-x-gmail.com wrote: > > Dear Dr. Davies, > > According to Gaussian manual and their book "Exploring chemistry with > electronic structure methods", "Low frequencies" list is *not* the actual > place where You should look for vibration modes. Probably You would bette= r > check table of frequency modes which is below the "Low frequencies" list > (starting with "Frequencies --") =E2=80=93 I am pretty sure that first va= lues > mentioned there meet well those in WebMO output. > For me, I did not ever considered what actually is printed in the "Low > frequencies" section, but, thank You, I see now these could be > translational/rotational modes. > > With best wishes, > Igors Mihailovs (engineer) > Institute of Solid State Physics > University of Latvia > > > 2014-12-11 17:51 GMT+02:00 Andrew Davies r.a.davies^-^bangor.ac.uk < > owner-chemistry+/-ccl.net>: >> >> >> Sent to CCL by: "Andrew Davies" [r.a.davies*bangor.ac.uk] >> During a recent Gaussian 09 run, we obtain the following low frequencies= : >> -7.3819 -6.1950 -3.9324 -0.0001 0.0007 0.0007 8.7154 19.6298 20.9237 >> >> When we analyse them using WebMO, it tells us that we have a 1st order T= S >> where the 1st imaginary (negative) frequency is -6.1950 cm-1. >> >> I understand that it has to choose 3 vibrational and 3 rotational modes >> > from the low frequencies list. Is there a reason why the programs "get >> rid >> of" specific frequencies. In this example, we lose the 1st, 3rd, 4th, 5t= h >> and 6th modes. Why can't we keep the the first two (giving a 2nd order T= S) >> and get rid of the next six? >> >> Regards, >> >> Dr. Andrew Davies >> School of Chemistry >> Bangor University >> UK >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY+/-ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST+/-ccl.net or use>> >> >> --047d7bb709ce3750be050a46b737 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dr. Davies,

The projection of translati= onal and rotational character out of the normal modes is a well-defined pro= cedure, and not an arbitrary selection of frequencies to retain/discard.=C2= =A0 Please see this link on Gaussian's website for more details about w= hat is done:=C2=A0ht= tp://www.gaussian.com/g_whitepap/vib.htm.

The = retention of the identical value of the imaginary frequency after projectio= n (-6.195 cm**-1 both before and after) is probably a numerical quirk of yo= ur system. In general, I would expect the value to change at least somewhat= after projection.=C2=A0

Also, with that small an = imaginary frequency, you probably are looking at an imperfectly optimized s= ystem with a very flat PES along one or more normal modes.=C2=A0 Do you per= chance have a methyl group or three in there, prone to internal rotation?


Best regards,
Brian
<= div>




On Mon, Dec 15, 2014 at 12:= 57 PM, Igors Mihailovs igor= s.mihailovs0-x-gmail.com <owner-chemistry###ccl.net>= wrote:
Dear Dr. D= avies,

According to Gaussian manual and their book "Explo= ring chemistry with electronic structure methods", "Low frequenci= es" list is not the actual place where You should look for vibr= ation modes. Probably You would better check table of frequency modes which= is below the "Low frequencies" list (starting with "Frequen= cies --") =E2=80=93 I am pretty sure that first values mentioned there= meet well those in WebMO output.
For me, I did not ever considere= d what actually is printed in the "Low frequencies" section, but,= thank You, I see now these could be translational/rotational modes.

With b= est wishes,
Igors Mihailovs (engineer)
Institute of S= olid State Physics
University of Latvia


2014-12-11 17:51 GMT+02:00 Andrew Davies r.a= .davies^-^bangor.ac.uk <owner-chemistry+/-ccl.net>:

Sent to CCL by: "Andrew=C2=A0 Davies" [r.a.davies*bangor.ac.uk]
During a recent Gaussian 09 run, we obtain the following low frequencies: -7.3819 -6.1950 -3.9324 -0.0001 0.0007 0.0007 8.7154 19.6298 20.9237

When we analyse them using WebMO, it tells us that we have a 1st order TS where the 1st imaginary (negative) frequency is -6.1950 cm-1.

I understand that it has to choose 3 vibrational and 3 rotational modes
> from the low frequencies list. Is there a reason why the programs &quo= t;get rid
of" specific frequencies. In this example, we lose the 1st, 3rd, 4th, = 5th
and 6th modes. Why can't we keep the the first two (giving a 2nd order = TS)
and get rid of the next six?

Regards,

Dr. Andrew Davies
School of Chemistry
Bangor University
UK



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--047d7bb709ce3750be050a46b737-- From owner-chemistry@ccl.net Mon Dec 15 16:16:00 2014 From: "conor douglas parks coparks2012*gmail.com" To: CCL Subject: CCL: Incorrect geometry generated using tinker newton minimization Message-Id: <-50821-141215135834-2173-Kug0PWvpHn1i1tXCxAt5Bw**server.ccl.net> X-Original-From: "conor douglas parks" Date: Mon, 15 Dec 2014 13:58:29 -0500 Sent to CCL by: "conor douglas parks" [coparks2012-,-gmail.com] Hello, I am currently trying to have my code write an initial tinker style xyz file, call the tinker newton.x executable with the oplsaa.prm file, and have it minimize an initial structure of tetrolic acid. When I ran it initially with all my molecules, the bonds were breaking. So as a check, I ran it just using one molecule. The following atom types were assigned from the olpsaa.prm file 209 3 C Carboxylic acid COOH 6 12.011 3 210 4 O Carboxylic acid C=O 8 15,.999 1 211 5 0H Carboxylic acid OH 8 15.999 2 212 7 HO Carboxylic acid COOH 1 1.008 769 19 CZ ALYKYNE RCCR 6 12.001 2 80 13 CT ALKANE CH3 6 12.001 4 85 46 HC ALKANE H-C 1 1.008 1 Using just the standard oplsaa.prm file, newton.x complains that the following is missing: undefined angle bending parameters: type atom names atom classes angle 2-CZ 3-CZ 4-C 19 19 3 angle 3-CZ 4-C 5-O 19 3 4 angle 3-CZ 4-C 6-OH 19 3 5 type atom names atom classes torsion 2-CZ 3-CZ 4-C 5-O 19 19 3 4 torsion 2-CZ 3-CZ 4-C 6-OH 19 19 3 5 torsion 3-CZ 4-C 6-OH 7-HO 19 3 5 7 So I went into the oplsaa.prm file I was using and added the parameters using what I took to be suitable approximations to the missing ones. The following approximations were made 19 19 3 ----> 19 19 13 19 3 4 ----> 13 3 4 19 3 5 ----> 13 3 5 For the time being, I have set the torsion values to zero since I haven't thought quite about what to do with them. I don't expect them to be particularly important for this molecule. However, I could be wrong. When I run energy minimization with this, the tinker routine seems to be spitting out an "incorrect" geometry. Specifically, the hydroxyl hydrogen has swung back to the carbon backbone chain as opposed to pointing out front of the molecule (sorry wish I could attach a picture). I ran the minimization with a 0.001 rms for the gradient, which should be sufficient. Does anyone have any idea what I can do to remedy this issue? Is there something wrong with the way I have approximated the angles? I am guessing there is potentially an imbalance between the parameters I have chosen, or maybe the molecular geometry is unstable. Any suggestion is appreciated From owner-chemistry@ccl.net Mon Dec 15 18:04:01 2014 From: "Luca Frediani luca.frediani%uit.no" To: CCL Subject: CCL: NMQC Conference Troms 11-15 Jan 2015. Last chance! Message-Id: <-50822-141215165846-22177-tFcmwB9DThq42skbZPsM/A++server.ccl.net> X-Original-From: "Luca Frediani" Date: Mon, 15 Dec 2014 16:58:45 -0500 Sent to CCL by: "Luca Frediani" [luca.frediani###uit.no] This is the last chance to register for the NMQC conference: online registration will close on Thursday the 18th. of December (5 spots left). The conference is dedicated to Real-Space Numerical Methods in Quantum Chemistry and will take place from the 11th to the 15th of January 2015 on board the Hurtigruten ship MS Midnattsol from Tromsoe to Kirkenes and back (Norway). Conference web site: http://www.ctcc.no/events/conferences/2015/numeric-conference/index.html Invited speakers: Thomas L Beck (University of Cincinnati, USA) Monica Bugeanu (University of Basel, Switzerland) Thierry Deutsch (INAC, Grenoble, France) Jussi Enkovaara (CSC - IT Center for Science, Espoo, Finland) Heinz-Juergen Flad ( Technische Universitt Mnchen, Germany) Luigi Genovese (INAC, Grenoble, France) Robert J Harrison (Stoony Brook University, USA) Venera Khoromskaia (Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany) Boris Khoromskij (Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany) Judith Rommel (University of Cambridge, UK) Hideo Sekino (Toyohashi University of Technology, Japan) Seiichiro Ten-No (Kobe University, Japan) Edward Valeev (Virginia Tech, USA) Correspondence regarding the conference may be addressed to luca.frediani-at-uit.no We hope to see you in Tromsoe in January! Best regards, Dage Sundholm and Luca Frediani