From owner-chemistry@ccl.net Mon Nov 3 07:53:01 2014 From: "Ali Fu arifnenu^^gmail.com" To: CCL Subject: CCL:G: Gaussian 09 - optimization (c4v point group of butadiene) Message-Id: <-50687-141103033730-15923-ozbKPj+hPPU8JvLVWHrDrQ*server.ccl.net> X-Original-From: "Ali Fu" Date: Mon, 3 Nov 2014 03:37:29 -0500 Sent to CCL by: "Ali Fu" [arifnenu ~ gmail.com] Hello everyone... I am a novice in gaussian calculations, I have tried to run optimization of cyclobutadiene with D4h/C4v symmetry (obtained in gaussview point group symmetry) with B3LYP/6-31G* basis set. But the output file modifies this to PG=D02H. How can I get the output same with the input PG=C04V? All responses, I will appreciate Ali Fu arifnenu^_^gmail.com From owner-chemistry@ccl.net Mon Nov 3 08:47:00 2014 From: "John Simmie john.simmie===nuigalway.ie" To: CCL Subject: CCL:G: Tweaking Gaussian to remove imaginay frequency Message-Id: <-50688-141103084557-24207-M1MiMgXOKAYoHhZlu/pFeA^_^server.ccl.net> X-Original-From: "John Simmie" Date: Mon, 3 Nov 2014 08:45:56 -0500 Sent to CCL by: "John Simmie" [john.simmie%%nuigalway.ie] In running a B3LYP/6-311G(2d,d,p) geometry/frequency calculation of the all-trans conformer of succinic acid 0,1 1 -2.350831000 2.938540000 0.000000000 8 -1.422415000 2.661642000 0.000000000 8 -2.436452000 0.657377000 0.000000000 6 -1.422415000 1.308099000 0.000000000 6 -0.015143000 0.761522000 0.000000000 1 0.511721000 1.167432000 0.867888000 1 0.511721000 1.167432000 -0.867888000 6 0.015143000 -0.761522000 0.000000000 1 -0.511721000 -1.167432000 -0.867888000 1 -0.511721000 -1.167432000 0.867888000 6 1.422415000 -1.308099000 0.000000000 8 2.436452000 -0.657377000 0.000000000 8 1.422415000 -2.661642000 0.000000000 1 2.350831000 -2.938540000 0.000000000 I end up with a imaginary frequency. Given THAT functional and basis set are there any general tweaks under Gaussian-09 that I can make which will eliminate it? Should one loosen or tighten limts or what? Opt-VTight does not help ... john.simmie at NUIGalway.ie From owner-chemistry@ccl.net Mon Nov 3 10:12:01 2014 From: "Igors Mihailovs igors.mihailovs0###gmail.com" To: CCL Subject: CCL:G: Tweaking Gaussian to remove imaginay frequency Message-Id: <-50689-141103101014-21071-0yLkiqAM0qxLZWBmhZc4cA{:}server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=001a11c3634e10d2bc0506f5be4f Date: Mon, 3 Nov 2014 17:09:48 +0200 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0,+,gmail.com] --001a11c3634e10d2bc0506f5be4f Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear John, This is not a matter of tweaking. Imaginary frequency indicates that Your geometry optimization is incomplete, You have actually find a saddle point. You should try altering Your initial geometry slightly, especially symmetry breaking may help a bit. Can You load Your results file to GaussView or Avogadro, or any other visualization program? What has usually helped me is starting an animation of vibration at this imaginary frequency =E2=80=93 th= e turning point geometry for this vibration is usually good initial guess for new geometry optimization. In GaussView, You can freeze it directly; in Avogadro I usually just pull appropriate atoms in the right direction, and this appears to be enough (maybe some additional optimization steps will be required). Best regards, Igors Mihailovs, ISSP, University of Latvia 2014-11-03 15:45 GMT+02:00 John Simmie john.simmie=3D=3D=3Dnuigalway.ie < owner-chemistry-x-ccl.net>: > > Sent to CCL by: "John Simmie" [john.simmie%%nuigalway.ie] > In running a B3LYP/6-311G(2d,d,p) geometry/frequency calculation of the > all-trans conformer of succinic acid > 0,1 > 1 -2.350831000 2.938540000 0.000000000 > 8 -1.422415000 2.661642000 0.000000000 > 8 -2.436452000 0.657377000 0.000000000 > 6 -1.422415000 1.308099000 0.000000000 > 6 -0.015143000 0.761522000 0.000000000 > 1 0.511721000 1.167432000 0.867888000 > 1 0.511721000 1.167432000 -0.867888000 > 6 0.015143000 -0.761522000 0.000000000 > 1 -0.511721000 -1.167432000 -0.867888000 > 1 -0.511721000 -1.167432000 0.867888000 > 6 1.422415000 -1.308099000 0.000000000 > 8 2.436452000 -0.657377000 0.000000000 > 8 1.422415000 -2.661642000 0.000000000 > 1 2.350831000 -2.938540000 0.000000000 > > I end up with a imaginary frequency. Given THAT functional and basis set > are there any general tweaks under Gaussian-09 that I can make which will > eliminate it? Should one loosen or tighten limts or what? Opt-VTight do= es > not help ... > > john.simmie at NUIGalway.ie > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a11c3634e10d2bc0506f5be4f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear John,

This is not a matter of tweak= ing. Imaginary frequency indicates that Your geometry optimization is incom= plete, You have actually find a saddle point. You should try altering Your = initial geometry slightly, especially symmetry breaking may help a bit. Can= You load Your results file to GaussView or Avogadro, or any other visualiz= ation program? What has usually helped me is starting an animation of vibra= tion at this imaginary frequency =E2=80=93 the turning point geometry for t= his vibration is usually good initial guess for new geometry optimization. = In GaussView, You can freeze it directly; in Avogadro I usually just pull a= ppropriate atoms in the right direction, and this appears to be enough (may= be some additional optimization steps will be required).



B= est regards,
Igors Mihailovs,
IS= SP, University of Latvia

=

2014-11-03 15:45 GMT+02:00 John Simmie john.= simmie=3D=3D=3Dnuigalway.ie <o= wner-chemistry-x-ccl.net>:
Sent to CCL by: "John=C2=A0 Simmie" [john.simmie%%nuigalway.ie]
In running a B3LYP/6-311G(2d,d,p) geometry/frequency calculation of the all= -trans conformer of succinic acid
0,1
1=C2=A0 =C2=A0 =C2=A0 =C2=A0-2.350831000=C2=A0 =C2=A0 =C2=A0 2.938540000=C2= =A0 =C2=A0 =C2=A0 0.000000000
8=C2=A0 =C2=A0 =C2=A0 =C2=A0-1.422415000=C2=A0 =C2=A0 =C2=A0 2.661642000=C2= =A0 =C2=A0 =C2=A0 0.000000000
8=C2=A0 =C2=A0 =C2=A0 =C2=A0-2.436452000=C2=A0 =C2=A0 =C2=A0 0.657377000=C2= =A0 =C2=A0 =C2=A0 0.000000000
6=C2=A0 =C2=A0 =C2=A0 =C2=A0-1.422415000=C2=A0 =C2=A0 =C2=A0 1.308099000=C2= =A0 =C2=A0 =C2=A0 0.000000000
6=C2=A0 =C2=A0 =C2=A0 =C2=A0-0.015143000=C2=A0 =C2=A0 =C2=A0 0.761522000=C2= =A0 =C2=A0 =C2=A0 0.000000000
1=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.511721000=C2=A0 =C2=A0 =C2=A0 1.167432000=C2= =A0 =C2=A0 =C2=A0 0.867888000
1=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.511721000=C2=A0 =C2=A0 =C2=A0 1.167432000=C2= =A0 =C2=A0 =C2=A0-0.867888000
6=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.015143000=C2=A0 =C2=A0 =C2=A0-0.761522000=C2= =A0 =C2=A0 =C2=A0 0.000000000
1=C2=A0 =C2=A0 =C2=A0 =C2=A0-0.511721000=C2=A0 =C2=A0 =C2=A0-1.167432000=C2= =A0 =C2=A0 =C2=A0-0.867888000
1=C2=A0 =C2=A0 =C2=A0 =C2=A0-0.511721000=C2=A0 =C2=A0 =C2=A0-1.167432000=C2= =A0 =C2=A0 =C2=A0 0.867888000
6=C2=A0 =C2=A0 =C2=A0 =C2=A0 1.422415000=C2=A0 =C2=A0 =C2=A0-1.308099000=C2= =A0 =C2=A0 =C2=A0 0.000000000
8=C2=A0 =C2=A0 =C2=A0 =C2=A0 2.436452000=C2=A0 =C2=A0 =C2=A0-0.657377000=C2= =A0 =C2=A0 =C2=A0 0.000000000
8=C2=A0 =C2=A0 =C2=A0 =C2=A0 1.422415000=C2=A0 =C2=A0 =C2=A0-2.661642000=C2= =A0 =C2=A0 =C2=A0 0.000000000
1=C2=A0 =C2=A0 =C2=A0 =C2=A0 2.350831000=C2=A0 =C2=A0 =C2=A0-2.938540000=C2= =A0 =C2=A0 =C2=A0 0.000000000

I end up with a imaginary frequency. Given THAT functional and basis set ar= e there any general tweaks under Gaussian-09 that I can make which will eli= minate it?=C2=A0 Should one loosen or tighten limts or what?=C2=A0 Opt-VTig= ht does not help ...

john.simmie at NUIGalway.ie



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY-x-ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEM= ISTRY-REQUEST-x-ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--001a11c3634e10d2bc0506f5be4f-- From owner-chemistry@ccl.net Mon Nov 3 10:46:00 2014 From: "Hao-Bo Guo guohaobo|*|gmail.com" To: CCL Subject: CCL:G: Tweaking Gaussian to remove imaginay frequency Message-Id: <-50690-141103100939-20933-DTdKt0mul30I2lpRF2Bdmg!=!server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=001a11c2d7ba6392480506f5bb82 Date: Mon, 3 Nov 2014 10:09:24 -0500 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo^gmail.com] --001a11c2d7ba6392480506f5bb82 Content-Type: text/plain; charset=UTF-8 My suggestion is to visualize the vibration with the imaginary frequency (the one with the highest amplitude); then re-optimize the structure starting from a snapshot obtained from the vibrational motion (but not the original geometry). The reason for doing this is that many optimizations may eventually end up at a two-states (or multi-states) vibration between two (or multiple) energy wells. You may check if this is the case by grep "SCF Done" the output file. BTW, the normal mode data can be used to yield structures of the vibration(s). A simple shell script can do this; gaussview may work as well. On Mon, Nov 3, 2014 at 8:45 AM, John Simmie john.simmie===nuigalway.ie < owner-chemistry__ccl.net> wrote: > > Sent to CCL by: "John Simmie" [john.simmie%%nuigalway.ie] > In running a B3LYP/6-311G(2d,d,p) geometry/frequency calculation of the > all-trans conformer of succinic acid > 0,1 > 1 -2.350831000 2.938540000 0.000000000 > 8 -1.422415000 2.661642000 0.000000000 > 8 -2.436452000 0.657377000 0.000000000 > 6 -1.422415000 1.308099000 0.000000000 > 6 -0.015143000 0.761522000 0.000000000 > 1 0.511721000 1.167432000 0.867888000 > 1 0.511721000 1.167432000 -0.867888000 > 6 0.015143000 -0.761522000 0.000000000 > 1 -0.511721000 -1.167432000 -0.867888000 > 1 -0.511721000 -1.167432000 0.867888000 > 6 1.422415000 -1.308099000 0.000000000 > 8 2.436452000 -0.657377000 0.000000000 > 8 1.422415000 -2.661642000 0.000000000 > 1 2.350831000 -2.938540000 0.000000000 > > I end up with a imaginary frequency. Given THAT functional and basis set > are there any general tweaks under Gaussian-09 that I can make which will > eliminate it? Should one loosen or tighten limts or what? Opt-VTight does > not help ... > > john.simmie at NUIGalway.ie> > > --001a11c2d7ba6392480506f5bb82 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
My suggestion is to visualize the vibration with the = imaginary frequency (the one with the highest amplitude); then re-optimize = the structure starting from a snapshot obtained from the vibrational motion= (but not the original geometry). The reason for doing this is that many op= timizations may eventually end up at a two-states (or multi-states) vibrati= on between two (or multiple) energy wells. You may check if this is the cas= e by grep "SCF Done" the output file.
BTW, the normal mo= de data can be used to yield structures of the vibration(s). A simple shell= script can do this; gaussview may work as well.

On Mon, Nov 3, 2014 at 8:45 AM, Jo= hn Simmie john.simmie=3D=3D=3Dnuigalway.ie<= /a> <owner-chemistry__ccl.net> wrote:

Sent to CCL by: "John=C2=A0 Simmie" [john.simmie%%nuigalway.ie]
In running a B3LYP/6-311G(2d,d,p) geometry/frequency calculation of the all= -trans conformer of succinic acid
0,1
1=C2=A0 =C2=A0 =C2=A0 =C2=A0-2.350831000=C2=A0 =C2=A0 =C2=A0 2.938540000=C2= =A0 =C2=A0 =C2=A0 0.000000000
8=C2=A0 =C2=A0 =C2=A0 =C2=A0-1.422415000=C2=A0 =C2=A0 =C2=A0 2.661642000=C2= =A0 =C2=A0 =C2=A0 0.000000000
8=C2=A0 =C2=A0 =C2=A0 =C2=A0-2.436452000=C2=A0 =C2=A0 =C2=A0 0.657377000=C2= =A0 =C2=A0 =C2=A0 0.000000000
6=C2=A0 =C2=A0 =C2=A0 =C2=A0-1.422415000=C2=A0 =C2=A0 =C2=A0 1.308099000=C2= =A0 =C2=A0 =C2=A0 0.000000000
6=C2=A0 =C2=A0 =C2=A0 =C2=A0-0.015143000=C2=A0 =C2=A0 =C2=A0 0.761522000=C2= =A0 =C2=A0 =C2=A0 0.000000000
1=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.511721000=C2=A0 =C2=A0 =C2=A0 1.167432000=C2= =A0 =C2=A0 =C2=A0 0.867888000
1=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.511721000=C2=A0 =C2=A0 =C2=A0 1.167432000=C2= =A0 =C2=A0 =C2=A0-0.867888000
6=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.015143000=C2=A0 =C2=A0 =C2=A0-0.761522000=C2= =A0 =C2=A0 =C2=A0 0.000000000
1=C2=A0 =C2=A0 =C2=A0 =C2=A0-0.511721000=C2=A0 =C2=A0 =C2=A0-1.167432000=C2= =A0 =C2=A0 =C2=A0-0.867888000
1=C2=A0 =C2=A0 =C2=A0 =C2=A0-0.511721000=C2=A0 =C2=A0 =C2=A0-1.167432000=C2= =A0 =C2=A0 =C2=A0 0.867888000
6=C2=A0 =C2=A0 =C2=A0 =C2=A0 1.422415000=C2=A0 =C2=A0 =C2=A0-1.308099000=C2= =A0 =C2=A0 =C2=A0 0.000000000
8=C2=A0 =C2=A0 =C2=A0 =C2=A0 2.436452000=C2=A0 =C2=A0 =C2=A0-0.657377000=C2= =A0 =C2=A0 =C2=A0 0.000000000
8=C2=A0 =C2=A0 =C2=A0 =C2=A0 1.422415000=C2=A0 =C2=A0 =C2=A0-2.661642000=C2= =A0 =C2=A0 =C2=A0 0.000000000
1=C2=A0 =C2=A0 =C2=A0 =C2=A0 2.350831000=C2=A0 =C2=A0 =C2=A0-2.938540000=C2= =A0 =C2=A0 =C2=A0 0.000000000

I end up with a imaginary frequency. Given THAT functional and basis set ar= e there any general tweaks under Gaussian-09 that I can make which will eli= minate it?=C2=A0 Should one loosen or tighten limts or what?=C2=A0 Opt-VTig= ht does not help ...

john.simmie at NUIGalway.ie



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY__ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEM= ISTRY-REQUEST__ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--001a11c2d7ba6392480506f5bb82-- From owner-chemistry@ccl.net Mon Nov 3 11:22:00 2014 From: "Igor Filippov igor.v.filippov . gmail.com" To: CCL Subject: CCL: use of research ideas without citation Message-Id: <-50691-141103104507-12014-MLGOo7+/4JcpIZMVUdpMig . server.ccl.net> X-Original-From: Igor Filippov Content-Type: multipart/alternative; boundary=f46d043bdf5ac34a680506f63a11 Date: Mon, 3 Nov 2014 10:45:01 -0500 MIME-Version: 1.0 Sent to CCL by: Igor Filippov [igor.v.filippov[-]gmail.com] --f46d043bdf5ac34a680506f63a11 Content-Type: text/plain; charset=UTF-8 I think this thread is getting out of control. Tom, I highly recommend you re-read the emails the others sent before, perhaps you will find significantly less encouragement and more caution and "please calm down" message. What misconduct are you talking about? Why anybody is supposed to apologize to you? If I got an email worded like this I would probably not bother reading it to the end. It is absolutely impossible to read all of the literature coming out in the field, I am getting invitations to submit to brand new journals weekly, if not daily. The titles sound respectable, even if I don't always recognize the publishers. If someone publishes there chances are I will never see this paper - this is academic misconduct to you? If this is all there is to it - someone developed a method identical to yours, completely independently and without being aware of your publications - then all I can say to you is be happy that your work was so good someone else went down the same path. Last, but not the least - the subject of this thread is "use of research ideas". Sorry to be blunt, but "ideas" are exceedingly cheap. It's the work that develops, supports and proves the idea which is valuable. Perhaps to some the reputation is "absolutely ridiculous" ( I quote), but others would prefer to be remembered for their work and not for crackpot accusations for developing ideas "which do not belong to them". As if ideas can belong to someone. Something to think about. Regards, Igor Sent to CCL by: "Felipe Pineda" [pideca55%a%gmail.com] Hi Tom: With all the pressure from "publish or perish" and the "impact factor" hype (originally a tool for librarians and not a measure of scientific productivity) it does not surprise me that such things happen. Scientific misconduct is not a felony, except if fraud can be demonstrated (before court). Therefore, your claims should be first proved. No problem with making them public. It's your right. Or maybe you should really worry about your reputation, as someone suggested - absolutely ridiculous: are we businessmen,banker, or manager, or are we scientists to care about reputation? What about the editors of the journals the papers were published in? Best, Felipe --f46d043bdf5ac34a680506f63a11 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I think this thread is getting out of control.
Tom, I highly recom= mend you re-read the emails the others sent before, perhaps you
will find= significantly less encouragement and more caution and "please calm do= wn" message.

= What misconduct are you talking about? Why anybody is supposed to=C2=A0apol= ogize=C2=A0to you?
If I g= ot an email worded like this I would probably not bother reading it to the = end.
It is absolutely imp= ossible to read all of the literature coming out in the field, I am getting=
invitations to submit to= brand new journals weekly, if not daily. The titles sound respectable, eve= n if I don't
always r= ecognize the publishers.=C2=A0If someone publishes there chances are
I will never see this paper - this is academic misco= nduct to you? If this is all there is to it - someone developed
a method identical to yours, complet= ely=C2=A0independently and without being aware of your publications=C2=A0- = then all
I can say to you= is be happy that your work was so good someone else went down the same pat= h.

= Last, but not the least - the subject of t= his thread is "use of research ideas". Sorry to be blunt, but &qu= ot;ideas" are=C2=A0
= exceedingly cheap. It's the work that develops, supports and proves the= idea which is valuable.
= Perhaps to some the reputation is "absolutely ridiculous" ( I quo= te), but others would prefer to be remembered for=C2=A0
their work and=C2=A0not for crackpot accusations for developing ide= as "which do not belong to them". As if ideas can
belong to someone. Something= to think about.

Rega= rds,
Igor



Sent to CCL = by: "Felipe=C2=A0 Pineda" [pideca55%a%gmail.com]
Hi Tom:

With all the pressure from "publish or perish&quo= t; and the "impact factor"
hype (originally a tool for librarians and not a measure of scie= ntific
productivity) it do= es not surprise me that such things happen.

Scientific misconduct is not a felony, except if fraud can be
demonstrated (before court). Therefore= , your claims should be first
proved. No problem with making them public. It's your right. Or may= be
you should really worry= about your reputation, as someone suggested -
absolutely ridiculous: are we businessmen,banker, or m= anager, or are we
scientis= ts to care about reputation?

What about the= editors of the journals the papers were published in?

Best,

Felipe
--f46d043bdf5ac34a680506f63a11-- From owner-chemistry@ccl.net Mon Nov 3 11:57:01 2014 From: "Close, David M. CLOSED^mail.etsu.edu" To: CCL Subject: CCL:G: Tweaking Gaussian to remove imaginay frequency Message-Id: <-50692-141103104857-15050-nDdxlT4yoLO+/uSz8p7RKg]![server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 3 Nov 2014 15:48:50 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED%x%mail.etsu.edu] John: "Tweaks Under Gaussian?" No. What you have to do is animate the frequency output to look at the particular vibration that involves this negative frequency. Then you have to make small changes in the coordinates of this motion in attempts to get off the optimization off this local minima in hopes of going towards the global minima. There are free programs on the internet to do this, and I can send one to you. But with a little practice you can guess at which numbers to alter. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu]_[ccl.net [mailto:owner-chemistry+closed==etsu.edu]_[ccl.net] On Behalf Of John Simmie john.simmie===nuigalway.ie Sent: Monday, November 03, 2014 8:46 AM To: Close, David M. Subject: CCL:G: Tweaking Gaussian to remove imaginay frequency Sent to CCL by: "John Simmie" [john.simmie%%nuigalway.ie] In running a B3LYP/6-311G(2d,d,p) geometry/frequency calculation of the all-trans conformer of succinic acid 0,1 1 -2.350831000 2.938540000 0.000000000 8 -1.422415000 2.661642000 0.000000000 8 -2.436452000 0.657377000 0.000000000 6 -1.422415000 1.308099000 0.000000000 6 -0.015143000 0.761522000 0.000000000 1 0.511721000 1.167432000 0.867888000 1 0.511721000 1.167432000 -0.867888000 6 0.015143000 -0.761522000 0.000000000 1 -0.511721000 -1.167432000 -0.867888000 1 -0.511721000 -1.167432000 0.867888000 6 1.422415000 -1.308099000 0.000000000 8 2.436452000 -0.657377000 0.000000000 8 1.422415000 -2.661642000 0.000000000 1 2.350831000 -2.938540000 0.000000000 I end up with a imaginary frequency. Given THAT functional and basis set are there any general tweaks under Gaussian-09 that I can make which will eliminate it? Should one loosen or tighten limts or what? Opt-VTight does not help ... john.simmie at NUIGalway.iehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Nov 3 12:32:01 2014 From: "Soren Eustis soreneustis]-[gmail.com" To: CCL Subject: CCL:G: Tweaking Gaussian to remove imaginay frequency Message-Id: <-50693-141103113729-3572-4QDIMzy0U5mzk0ei7W94hQ.:.server.ccl.net> X-Original-From: Soren Eustis Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Mon, 03 Nov 2014 11:37:18 -0500 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis^-^gmail.com] John, You can try to make a small displacement along the coordinate of the imaginary mode. Otherwise, try int=ultrafine. However, you cannot compare jobs with and without this keyword, so you would need to commit to this change across the project. Soren On 11/3/14, 8:45 AM, "John Simmie john.simmie===nuigalway.ie" wrote: > >Sent to CCL by: "John Simmie" [john.simmie%%nuigalway.ie] >In running a B3LYP/6-311G(2d,d,p) geometry/frequency calculation of the >all-trans conformer of succinic acid >0,1 >1 -2.350831000 2.938540000 0.000000000 >8 -1.422415000 2.661642000 0.000000000 >8 -2.436452000 0.657377000 0.000000000 >6 -1.422415000 1.308099000 0.000000000 >6 -0.015143000 0.761522000 0.000000000 >1 0.511721000 1.167432000 0.867888000 >1 0.511721000 1.167432000 -0.867888000 >6 0.015143000 -0.761522000 0.000000000 >1 -0.511721000 -1.167432000 -0.867888000 >1 -0.511721000 -1.167432000 0.867888000 >6 1.422415000 -1.308099000 0.000000000 >8 2.436452000 -0.657377000 0.000000000 >8 1.422415000 -2.661642000 0.000000000 >1 2.350831000 -2.938540000 0.000000000 > >I end up with a imaginary frequency. Given THAT functional and basis set >are there any general tweaks under Gaussian-09 that I can make which will >eliminate it? Should one loosen or tighten limts or what? Opt-VTight >does not help ... > >john.simmie at NUIGalway.ie> > From owner-chemistry@ccl.net Mon Nov 3 13:07:01 2014 From: "Cina Foroutan-Nejad canyslopus*yahoo.co.uk" To: CCL Subject: CCL:G: Gaussian 09 - optimization (c4v point group of butadiene) Message-Id: <-50694-141103115311-17253-IhkElAoyyukVXAuG7gkWDQ**server.ccl.net> X-Original-From: Cina Foroutan-Nejad Content-Type: multipart/alternative; boundary="2029223015-1165890561-1415033570=:72457" Date: Mon, 3 Nov 2014 16:52:50 +0000 MIME-Version: 1.0 Sent to CCL by: Cina Foroutan-Nejad [canyslopus-*-yahoo.co.uk] --2029223015-1165890561-1415033570=:72457 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Ali,=0A=0ACyclobutadiene local minimum structure is indeed D_2h not D4h.= So, if you are looking for the local minimum structure, you already did yo= ur job well. =0AThe D4h structure is a TS (one imaginary frequency) and you= may not get it with DFT or any other single reference method. For optimizi= ng D4h structure that is a text book example of a molecule with multirefere= nce character you must run your calculations at (at least) CAS(4,4) computa= tional level. =0A=0AGood luck =0ACina=0A=0A--------------------------------= ----=0ACina Foroutan-Nejad, PhD=0ANational Center for Biomolecular Research= ,=0AMasaryk University, Brno,=0ACzech Republic=0Ahttps://muni.academia.edu/= CinaForoutanNejad=0A=0A=0A=0AOn Monday, 3 November 2014, 16:17, Ali Fu arif= nenu^^gmail.com wrote:=0A =0A=0A=0A=0ASent to CCL= by: "Ali Fu" [arifnenu ~ gmail.com]=0AHello everyone...=0AI am a novice = in gaussian calculations, I have tried to run optimization =0Aof cyclobutad= iene with D4h/C4v symmetry (obtained in gaussview point group =0Asymmetry) = with B3LYP/6-31G* basis set. But the output file modifies this to =0APG=3DD= 02H. How can I get the output same with the input PG=3DC04V? =0AAll respons= es, I will appreciate=0A=0AAli Fu=0Aarifnenu**gmail.com=0A=0A=0A=0A-=3D Thi= s is automatically added to each message by the mailing script =3D-=0ATo re= cover the email address of the author of the message, please change=0Athe s= trange characters on the top line to the (-) sign. You can also=0Alook up the= X-Original-From: line in the mail header.=0A=0AE-mail to subscribers: CHEM= ISTRY(-)ccl.net or use:=0A http://www.ccl.net/cgi-bin/ccl/send_ccl_messa= ge=0A=0A=0A ==0A=0ASubscribe/Unsubscribe:= =0A=0A=0ABefore posting,= check wait time at: http://www.ccl.net=0A=0A= =0A= =0A=0A= =0A=0A=0A http:/= /www.ccl.net/spammers.txt=0A=0ARTFI: http://www.ccl.net/chemistry/aboutccl/= instructions/ --2029223015-1165890561-1415033570=:72457 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi Ali,

<= /div>
Cyclobutadiene local minimum structure is ind= eed D_2h not D4h. So, if you are looking for the local minimum structure, y= ou already did your job well. 
The D4h s= tructure is a TS (one imaginary frequency) and you may not get it with DFT = or any other single reference method. For optimizing D4h structure that is = a text book example of a molecule with multireference character you must ru= n your calculations at (at least) CAS(4,4) computational level. 

Good luck 
Cina

-----------------------= -------------
Cina Foroutan-Nejad, PhD
<= div style=3D"color: rgb(0, 0, 0); font-size: 16px; font-family: 'bookman ol= d style', 'new york', times, serif; font-style: normal; background-color: t= ransparent;" class=3D"">National Center for Biomolecular Research,
Masaryk University, Brno,
Czech Republic
https://muni.academia.edu/CinaForoutanNejad
<= /div>


On Monday, 3 Novem= ber 2014, 16:17, Ali Fu arifnenu^^gmail.com <owner-chemistry(-)ccl.net>= wrote:



Sent to CCL by: "Ali  Fu" [arifnenu ~ gmail.com]
Hello everyone...
I am a novice  = in gaussian calculations, I have tried to run optimization
of cyclobutadiene with D4h/C4v symmetry (obtaine= d in gaussview point group
symmetry) with B3LYP/6= -31G* basis set. But the output file modifies this to
PG=3DD02H. How can I get the output same with the input PG=3DC04V? All responses, I will appreciate

Ali Fu
arifnenu**= gmail.com



-=3D This is automatically added to e= ach message by the mailing script =3D-
To recover = the email address of the author of the message, please change
the strange characters on the top line to the (-) sign. You can a= lso
look up the X-Original-From: line in the mail = header.

E-mail to subscr= ibers: CHEMISTRY(-)ccl.net<= /a> or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST(-)ccl.net or use
      http://www.ccl.net= /cgi-bin/ccl/send_ccl_message

    &n= bsp; http://www.ccl.net/chemistry/sub_unsub.shtml=

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/ch= emistry/announcements/conferences/

Search Messages: http://www.cc= l.net/chemistry/searchccl/index.shtml

      http://www.ccl.net/spa= mmers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructio= ns/




--2029223015-1165890561-1415033570=:72457-- From owner-chemistry@ccl.net Mon Nov 3 14:44:01 2014 From: "Adam Tenderholt atenderholt%gmail.com" To: CCL Subject: CCL:G: Tweaking Gaussian to remove imaginay frequency Message-Id: <-50695-141103144044-17841-APXAUPT2ISiNCRvfz8GO2A_._server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=001a11c13062c881e10506f98439 Date: Mon, 3 Nov 2014 11:40:07 -0800 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt---gmail.com] --001a11c13062c881e10506f98439 Content-Type: text/plain; charset=UTF-8 As other's have mentioned, you can try visualizing the imaginary mode and re-optimizing after a slight displacement along that coordinate. One software tool for this is QMForge (http://qmforge.sourceforge.net/) which has a "tab" for analyzing frequency calculations where both animations and individual structures along a mode can be saved. Adam Disclaimer: I'm the developer of QMForge. As always, comments and suggestions for improvement welcome. On Mon, Nov 3, 2014 at 8:37 AM, Soren Eustis soreneustis]-[gmail.com < owner-chemistry(0)ccl.net> wrote: > > Sent to CCL by: Soren Eustis [soreneustis^-^gmail.com] > John, > > You can try to make a small displacement along the coordinate of the > imaginary mode. Otherwise, try int=ultrafine. However, you cannot > compare jobs with and without this keyword, so you would need to commit to > this change across the project. > > Soren > > On 11/3/14, 8:45 AM, "John Simmie john.simmie===nuigalway.ie" > wrote: > > > > >Sent to CCL by: "John Simmie" [john.simmie%%nuigalway.ie] > >In running a B3LYP/6-311G(2d,d,p) geometry/frequency calculation of the > >all-trans conformer of succinic acid > >0,1 > >1 -2.350831000 2.938540000 0.000000000 > >8 -1.422415000 2.661642000 0.000000000 > >8 -2.436452000 0.657377000 0.000000000 > >6 -1.422415000 1.308099000 0.000000000 > >6 -0.015143000 0.761522000 0.000000000 > >1 0.511721000 1.167432000 0.867888000 > >1 0.511721000 1.167432000 -0.867888000 > >6 0.015143000 -0.761522000 0.000000000 > >1 -0.511721000 -1.167432000 -0.867888000 > >1 -0.511721000 -1.167432000 0.867888000 > >6 1.422415000 -1.308099000 0.000000000 > >8 2.436452000 -0.657377000 0.000000000 > >8 1.422415000 -2.661642000 0.000000000 > >1 2.350831000 -2.938540000 0.000000000 > > > >I end up with a imaginary frequency. Given THAT functional and basis set > >are there any general tweaks under Gaussian-09 that I can make which will > >eliminate it? Should one loosen or tighten limts or what? Opt-VTight > >does not help ... > > > >john.simmie at NUIGalway.ie> > > --001a11c13062c881e10506f98439 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
As other's have mentioned, you can try visualizing the= imaginary mode and re-optimizing after a slight displacement along that co= ordinate. One software tool for this is QMForge (http://qmforge.sourceforge.net/) which has a "ta= b" for analyzing frequency calculations where both animations and indi= vidual structures along a mode can be saved.

Adam
<= div>
Disclaimer: I'm the developer of QMForge. As always,= comments and suggestions for improvement welcome.


On Mon, Nov 3, = 2014 at 8:37 AM, Soren Eustis soreneustis]-[gm= ail.com <owner-chemistry(0)ccl.net> wrote:

Sent to CCL by: Soren Eustis [soreneustis^-^gmail.com]
John,

=C2=A0 =C2=A0You can try to make a small displacement along the coordinate = of the
imaginary mode.=C2=A0 Otherwise, try int=3Dultrafine.=C2=A0 However, you ca= nnot
compare jobs with and without this keyword, so you would need to commit to<= br> this change across the project.

Soren

On 11/3/14, 8:45 AM, "John Simmie john.simmie=3D=3D=3Dnuigalway.ie"
<owner-chemistry{}ccl.net> wrote:

>
>Sent to CCL by: "John=C2=A0 Simmie" [john.simmie%%nuigalway.ie]
>In running a B3LYP/6-311G(2d,d,p) geometry/frequency calculation of the=
>all-trans conformer of succinic acid
>0,1
>1=C2=A0 =C2=A0 =C2=A0 =C2=A0-2.350831000=C2=A0 =C2=A0 =C2=A0 2.93854000= 0=C2=A0 =C2=A0 =C2=A0 0.000000000
>8=C2=A0 =C2=A0 =C2=A0 =C2=A0-1.422415000=C2=A0 =C2=A0 =C2=A0 2.66164200= 0=C2=A0 =C2=A0 =C2=A0 0.000000000
>8=C2=A0 =C2=A0 =C2=A0 =C2=A0-2.436452000=C2=A0 =C2=A0 =C2=A0 0.65737700= 0=C2=A0 =C2=A0 =C2=A0 0.000000000
>6=C2=A0 =C2=A0 =C2=A0 =C2=A0-1.422415000=C2=A0 =C2=A0 =C2=A0 1.30809900= 0=C2=A0 =C2=A0 =C2=A0 0.000000000
>6=C2=A0 =C2=A0 =C2=A0 =C2=A0-0.015143000=C2=A0 =C2=A0 =C2=A0 0.76152200= 0=C2=A0 =C2=A0 =C2=A0 0.000000000
>1=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.511721000=C2=A0 =C2=A0 =C2=A0 1.16743200= 0=C2=A0 =C2=A0 =C2=A0 0.867888000
>1=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.511721000=C2=A0 =C2=A0 =C2=A0 1.16743200= 0=C2=A0 =C2=A0 =C2=A0-0.867888000
>6=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.015143000=C2=A0 =C2=A0 =C2=A0-0.76152200= 0=C2=A0 =C2=A0 =C2=A0 0.000000000
>1=C2=A0 =C2=A0 =C2=A0 =C2=A0-0.511721000=C2=A0 =C2=A0 =C2=A0-1.16743200= 0=C2=A0 =C2=A0 =C2=A0-0.867888000
>1=C2=A0 =C2=A0 =C2=A0 =C2=A0-0.511721000=C2=A0 =C2=A0 =C2=A0-1.16743200= 0=C2=A0 =C2=A0 =C2=A0 0.867888000
>6=C2=A0 =C2=A0 =C2=A0 =C2=A0 1.422415000=C2=A0 =C2=A0 =C2=A0-1.30809900= 0=C2=A0 =C2=A0 =C2=A0 0.000000000
>8=C2=A0 =C2=A0 =C2=A0 =C2=A0 2.436452000=C2=A0 =C2=A0 =C2=A0-0.65737700= 0=C2=A0 =C2=A0 =C2=A0 0.000000000
>8=C2=A0 =C2=A0 =C2=A0 =C2=A0 1.422415000=C2=A0 =C2=A0 =C2=A0-2.66164200= 0=C2=A0 =C2=A0 =C2=A0 0.000000000
>1=C2=A0 =C2=A0 =C2=A0 =C2=A0 2.350831000=C2=A0 =C2=A0 =C2=A0-2.93854000= 0=C2=A0 =C2=A0 =C2=A0 0.000000000
>
>I end up with a imaginary frequency. Given THAT functional and basis se= t
>are there any general tweaks under Gaussian-09 that I can make which wi= ll
>eliminate it?=C2=A0 Should one loosen or tighten limts or what?=C2=A0 O= pt-VTight
>does not help ...
>
>john.simmie at NUIGalway.ie>
>



-=3D This is automatically a= dded to each message by the mailing script =3D-
E-mail to subscribers: CHEMISTRY(0)ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEM= ISTRY-REQUEST(0)ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--001a11c13062c881e10506f98439-- From owner-chemistry@ccl.net Mon Nov 3 17:15:01 2014 From: "Ramy EHab Farag romio.1001=-=yahoo.com" To: CCL Subject: CCL:G: Material studio Vs Gaussian Message-Id: <-50696-141103171006-15703-p85mjlaaDXVpalte51sliQ- -server.ccl.net> X-Original-From: "Ramy EHab Farag" Date: Mon, 3 Nov 2014 17:10:05 -0500 Sent to CCL by: "Ramy EHab Farag" [romio.1001#%#yahoo.com] I have 2 questions : 1- In material studio program , can i submit a job from it to Gaussian09 ? 2- In doping systems : how to choose a dopant atom in anatase crystal and how to make it using any program ? From owner-chemistry@ccl.net Mon Nov 3 17:50:01 2014 From: "Laurence Patrick Cuffe cuffe[a]mac.com" To: CCL Subject: CCL: use of research ideas without citation Message-Id: <-50697-141103173441-24635-cy9PbAnPL6H0G4Vcf8VcmA : server.ccl.net> X-Original-From: "Laurence Patrick Cuffe" Date: Mon, 3 Nov 2014 17:34:40 -0500 Sent to CCL by: "Laurence Patrick Cuffe" [cuffe{:}mac.com] Igor, I beg to disagree. 2 minutes searching with google on the key terms in the plagiarising paper found Toms paper. While I have a lot of respect for at least one of the authors of the offending paper, in this case I think they are out of line. All the best Dr. Laurence Cuffe From owner-chemistry@ccl.net Mon Nov 3 20:24:01 2014 From: "Di Fan happy.fandi||163.com" To: CCL Subject: CCL: Help for corrected Linear Responds (cLR) - PCMoption Message-Id: <-50698-141103201121-27593-xBcofD9mlksDMLX78CYRxQ.@.server.ccl.net> X-Original-From: "Di Fan" Date: Mon, 3 Nov 2014 20:11:20 -0500 Sent to CCL by: "Di Fan" [happy.fandi*|*163.com] Dears, I have done the linear responds (LR) PCM and the specific state (SS) PCM to a molecular with a veriety of solvents. I can't sure if the SS change the ground state referance during the optimization process of the excited state cavity,because it might lead to unphysical values when the charge transfer is extreme. I want to check the result by corrected linear responds (cLR) PCM scheme that is also available in G09.D, but I am introble to set the key words. If I only want to calculate the single point energy of the optical LR-PCM geometry, how should I set up in the keywords? Could you be kind enough to help me? Thanks in advance. Best regards. DiFan E-mail:happy.fandi^^^163.com