From owner-chemistry@ccl.net Sat May 22 00:31:00 2010 From: "Deepak Ojha alwaysinthemind ~~ gmail.com" To: CCL Subject: CCL: Why Magnon Is A Boson Message-Id: <-41912-100522003008-22574-rrywwblmWNfTIHntHQ+4RQ**server.ccl.net> X-Original-From: Deepak Ojha Content-Type: multipart/alternative; boundary=000e0cd1750ed7d43f0487274223 Date: Sat, 22 May 2010 10:00:01 +0530 MIME-Version: 1.0 Sent to CCL by: Deepak Ojha [alwaysinthemind..gmail.com] --000e0cd1750ed7d43f0487274223 Content-Type: text/plain; charset=ISO-8859-1 Hi All I had been going through the details of Spin Wave Theory and Holstein Primikoff Transformation meant to study magnetism at low temperatures.spin sites basically being electrons are supposed to behave like fermions but HP Transformation leads them to behave like bosons. Can anyone tell me the facts underneath. -- DeepaK Ojha School Of Chemistry "Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live" --000e0cd1750ed7d43f0487274223 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All
I had been going through the details of Spin Wave Theory and Hols= tein Primikoff
Transformation meant to study magnetism at low temperatur= es.spin sites basically
being electrons are supposed to behave like ferm= ions but HP Transformation
leads them to behave like bosons.

Can anyone tell me the facts under= neath.

--
DeepaK Ojha
School Of Chemistry
"Selfishness is not living as one wishes to live, it is asking other= s to live as one wishes to live"
--000e0cd1750ed7d43f0487274223-- From owner-chemistry@ccl.net Sat May 22 10:05:00 2010 From: "Vigneshwar Ramakrishnan vmsrvignesh++gmail.com" To: CCL Subject: CCL:G: Gaussian Error in Internal coordinates Message-Id: <-41913-100522043417-15975-DzBlHoqvt+P3281U3zTEAQ..server.ccl.net> X-Original-From: "Vigneshwar Ramakrishnan" Date: Sat, 22 May 2010 04:34:15 -0400 Sent to CCL by: "Vigneshwar Ramakrishnan" [vmsrvignesh##gmail.com] Dear All, I am using (actually, learning!) Gaussian to investigate the properties of DNA. I generated a 2bp-DNA structure and submitted the *.com file with ROM062X/3-21G method. However, I get the following error when the job runs. Could anyone please help me understand the meaning of this error message and give pointers as to how to fix it? Cartesian Forces: Max 0.107961092 RMS 0.021734872 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. NTrRot= -1 NTRed= 730 NAtoms= 126 NSkip= 358 IsLin=F Error in internal coordinate system. Error termination via Lnk1e in /app1/em64t/g09/l103.exe at Sat May 22 16:05:45 2010. Job cpu time: 0 days 0 hours 0 minutes 2.9 seconds. Thank you very much, Sincerely, Vignesh Graduate Student, Dept. of Chem and Biomolecular Engg, National University of Singapore. Singapore. From owner-chemistry@ccl.net Sat May 22 10:39:00 2010 From: "Ol Ga eurisco1]_[pochta.ru" To: CCL Subject: CCL: odd geomertries Message-Id: <-41914-100522100833-1357-IUvi+NwhUtjJ9X94q3glPw||server.ccl.net> X-Original-From: "Ol Ga" Date: Sat, 22 May 2010 10:08:32 -0400 Sent to CCL by: "Ol Ga" [eurisco1 : pochta.ru] Dear zouzou adnani, 1) You should check the multiplycity. Possible, It is not 1. 2) You should be sure that the geometry of the system converged to a stationary point (it is comment about Maxcycle) 3) You should change slightly the input (possible other ECP for Fe will be suitable): opt b3lyp/gen pseudo=read guess=save From owner-chemistry@ccl.net Sat May 22 11:14:00 2010 From: "mohamed aish mhmdaish-*-yahoo.com" To: CCL Subject: CCL: odd geomertries Message-Id: <-41915-100521233206-1433-cbLXTd1yHGWmheX/nmW3rA/a\server.ccl.net> X-Original-From: mohamed aish Content-Type: multipart/alternative; boundary="0-305590115-1274499118=:37072" Date: Fri, 21 May 2010 20:31:58 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: mohamed aish [mhmdaish(-)yahoo.com] --0-305590115-1274499118=:37072 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi; Your input should be as follows; =A0 # opt b3lyp/gen pseudo=3Dread guess=3Dsave=20 . 0 1 (z-matrix) C,H,N,O 0 6-31g(d,p) **** Fe 0 cep-121g **** Blank Fe 0 cep-121g no stars =A0 Good luck --- On Sat, 5/22/10, zouzou adnani zinebeladnani]^[hotmail.com wrote: > From: zouzou adnani zinebeladnani]^[hotmail.com Subject: CCL: odd geomertries To: "Aish, Mhmd Ahmd " Received: Saturday, May 22, 2010, 3:25 AM Sent to CCL by: "zouzou=A0 adnani" [zinebeladnani~!~hotmail.com] HI everyone, I'm working on the computational study of interactions between iron atom an= d some quinoxaline derivatives. every time I end up with very odd geometrie= s.=20 this is my input file: # opt b3lyp/gen pseudo=3Dread guess=3Dsave=20 . 0 1 (z-matrix) C H N O 0 6-31g(d,p) **** Fe 0 cep-121g **** I tried to modify the iron position and I used different values of Maxcycle= but it's not working=20 I'm running out of time and I'm completely lost please help me thanks -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A --0-305590115-1274499118=:37072 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi;
Your input should be as follows;
 
# opt b3lyp/gen pseudo=3Dread guess=3Dsave
.
0 1
(z-matrix)<= BR>
C,H,N,O 0
6-31g(d,p)
****
Fe 0
cep-121g
****
Blank=
Fe 0
cep-121g
no stars

 
Good luck

--- On Sat, 5/22/10, zouzou adnani zinebeladnani]^[hotmail.com = <owner-chemistry#ccl.net> wrote:

From: zouzou adnani zinebeladnani]^[hotmail.com &= lt;owner-chemistry#ccl.net>
Subject: CCL: odd geomertries
To: "Ais= h, Mhmd Ahmd " <mhmdaish#yahoo.com>
Received: Saturday, Ma= y 22, 2010, 3:25 AM


Sent to CCL by: "zouzou  adnani" [zinebelad= nani~!~hotmail.com]
HI everyone,
I'm working on the computational stu= dy of interactions between iron atom and some quinoxaline derivatives. ever= y time I end up with very odd geometries.
this is my input file:
# opt b3lyp/gen pseudo=3Dread guess=3Dsave
.
0 1
(z-matrix)
<= BR>C H N O 0
6-31g(d,p)
****


Fe 0
cep-121g
****
<= BR>I tried to modify the iron position and I used different values of Maxcy= cle but it's not working
I'm running out of time and I'm completely los= t please help me
thanks



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<= br> --0-305590115-1274499118=:37072-- From owner-chemistry@ccl.net Sat May 22 11:52:00 2010 From: "Ol Ga eurisco1{}pochta.ru" To: CCL Subject: CCL:G: Gaussian Error in Internal coordinates Message-Id: <-41916-100522112304-20364-TdA+LrDU596r+QK4aypBYA/./server.ccl.net> X-Original-From: "Ol Ga" Date: Sat, 22 May 2010 11:22:55 -0400 Sent to CCL by: "Ol Ga" [eurisco1[]pochta.ru] Dear Vigneshwar Ramakrishnan, I observed this error. It depends on both options - method + basis. If you choose the level of theory, you should change some positions of atoms - increase slightly some bond lengths. I made this tune of my "tight" structure (changed position of 6 atoms from 100 atoms) and new "expanded" structure converged smoothly without this error. Anyway, you can optimize your structure on other level and than start the optimization at the desired level of theory from previously optimized point. It is an option. Sincerely, Ol Ga -------------------------------------------------- > From: "Vigneshwar Ramakrishnan vmsrvignesh++gmail.com" Sent: Saturday, May 22, 2010 12:34 PM To: "Ga, Ol " Subject: CCL:G: Gaussian Error in Internal coordinates > > > Sent to CCL by: "Vigneshwar Ramakrishnan" [vmsrvignesh##gmail.com] > Dear All, > > I am using (actually, learning!) Gaussian to investigate the properties of DNA. I generated a 2bp-DNA structure and submitted the *.com file with ROM062X/3-21G method. However, I get the following error when the job runs. Could anyone please help me understand the meaning of this error message and give pointers as to how to fix it? > > Cartesian Forces: Max 0.107961092 RMS 0.021734872 > > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > Berny optimization. > NTrRot= -1 NTRed= 730 NAtoms= 126 NSkip= 358 IsLin=F > Error in internal coordinate system. > Error termination via Lnk1e in /app1/em64t/g09/l103.exe at Sat May 22 16:05:45 2010. > Job cpu time: 0 days 0 hours 0 minutes 2.9 seconds. > > > Thank you very much, > Sincerely, > Vignesh > > Graduate Student, > Dept. of Chem and Biomolecular Engg, > National University of Singapore. > Singapore. > > > From owner-chemistry@ccl.net Sat May 22 12:27:00 2010 From: "W. Flak williamflak*|*yahoo.com" To: CCL Subject: CCL: Negative Frequency Message-Id: <-41917-100522121739-4746-MmidQXK+hcnisbdZze8wDg%a%server.ccl.net> X-Original-From: "W. Flak" Date: Sat, 22 May 2010 12:17:37 -0400 Sent to CCL by: "W. Flak" [williamflak^^yahoo.com] Dear CCL I have optimized my molecule using B3LYP/6-311++G**, during freq step I got -50 negative frequency. The same job has been optimized basing on B3LYP/6-31G* and gave me a negative frequency at -19 I remember I read a paper/book saying this low frequencies could be ignored. Is that right? This negative frequency is due you to planar two aromatic rings (like biphenyl). Should I ignore it and go on? Any kind of help would be appreciated. Thanks in advance W. Flak From owner-chemistry@ccl.net Sat May 22 13:37:00 2010 From: "Ol Ga eurisco1]-[pochta.ru" To: CCL Subject: CCL: Negative Frequency Message-Id: <-41918-100522125715-7662-FODmIU5Hak10QmcKSfHBig(-)server.ccl.net> X-Original-From: "Ol Ga" Date: Sat, 22 May 2010 12:57:12 -0400 Sent to CCL by: "Ol Ga" [eurisco1[#]pochta.ru] Dear W. Flak, I suggest you to make optimization in your case with more aggressive criteria of local minima search. You should clarify what software do you use. To ignore imaginary freq you should be sure that it is only a numerical error. Possible you need also increase grid for DFT. Sincerely, Ol Ga -------------------------------------------------- > From: "W. Flak williamflak*|*yahoo.com" Sent: Saturday, May 22, 2010 8:17 PM To: "Ga, Ol " Subject: CCL: Negative Frequency > > > Sent to CCL by: "W. Flak" [williamflak^^yahoo.com] > Dear CCL > I have optimized my molecule using B3LYP/6-311++G**, during freq step I got -50 > negative frequency. > The same job has been optimized basing on B3LYP/6-31G* and gave me a negative > frequency at -19 > I remember I read a paper/book saying this low frequencies could be ignored. Is > that right? > This negative frequency is due you to planar two aromatic rings (like > biphenyl). > Should I ignore it and go on? > Any kind of help would be appreciated. > Thanks in advance > W. Flak > > > From owner-chemistry@ccl.net Sat May 22 17:26:01 2010 From: "partha kundu partha1kundu{:}yahoo.com" To: CCL Subject: CCL: Negative Frequency Message-Id: <-41919-100522172329-2100-9JxLU2jqi67t1Yaa3/9i8Q===server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary="0-1742517475-1274563397=:5566" Date: Sun, 23 May 2010 02:53:17 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu=-=yahoo.com] --0-1742517475-1274563397=:5566 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable You can try the following: Distort the molecule along the arrow of the=A0 mode which is giving negativ= e frequency. Then reoptimize. =A0regards. Partha. --- On Sat, 22/5/10, W. Flak williamflak*|*yahoo.com wrote: > From: W. Flak williamflak*|*yahoo.com Subject: CCL: Negative Frequency To: "Kundu, Partha Pratim " Date: Saturday, 22 May, 2010, 9:47 PM Sent to CCL by: "W.=A0 Flak" [williamflak^^yahoo.com] Dear CCL I have optimized my molecule using B3LYP/6-311++G**, during freq step I got= -50=20 negative frequency. The same job has been optimized basing on B3LYP/6-31G* and gave me a negati= ve=20 frequency at -19 I remember I read a paper/book saying this low frequencies could be ignored= . Is=20 that right? This negative frequency is due you to planar two aromatic rings (like=20 biphenyl). Should I ignore it and go on? Any kind of help would be appreciated. Thanks in advance W. Flak -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A --0-1742517475-1274563397=:5566 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable <= /table>
--0-1742517475-1274563397=:5566-- From owner-chemistry@ccl.net Sat May 22 22:19:00 2010 From: "Robert Kolakowski robertk[-]scripps.edu" To: CCL Subject: CCL: Negative Frequency Message-Id: <-41920-100522145334-3170-Z9TJZpS2khAePrFFiXvhmg{=}server.ccl.net> X-Original-From: Robert Kolakowski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes Date: Sat, 22 May 2010 11:53:23 -0700 MIME-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Robert Kolakowski [robertk^-^scripps.edu] Dear Flak, I think the best way to solve this problem is to visualize the vibration and see if it has anything to do with the TS. If not they can usually be ignored. You often can get some negative frequencies from weak vibrations like rotations around a methyl group etc. They can be very difficult to remove. But a tighter optimization can help. Cheers, Rob ____________________ Robert V. Kolakowski, Ph. D. Post Doc, K. C. Nicolaou Lab The Scripps Research Institute La Jolla, CA 92037 Laboratory Tel. 858.784.2480 On May 22, 2010, at 9:57 AM, Ol Ga eurisco1]-[pochta.ru wrote: > > Sent to CCL by: "Ol Ga" [eurisco1[#]pochta.ru] > Dear W. Flak, > > I suggest you to make optimization in your case with more aggressive > criteria of local minima search. > You should clarify what software do you use. To ignore imaginary > freq you should be sure that it is only a numerical error. Possible > you need also increase grid for DFT. > > > Sincerely, > Ol Ga > > > > -------------------------------------------------- >> From: "W. Flak williamflak*|*yahoo.com" > Sent: Saturday, May 22, 2010 8:17 PM > To: "Ga, Ol " > Subject: CCL: Negative Frequency > >> >> >> Sent to CCL by: "W. Flak" [williamflak^^yahoo.com] >> Dear CCL >> I have optimized my molecule using B3LYP/6-311++G**, during freq >> step I got -50 >> negative frequency. >> The same job has been optimized basing on B3LYP/6-31G* and gave me >> a negative >> frequency at -19 >> I remember I read a paper/book saying this low frequencies could be >> ignored. Is >> that right? >> This negative frequency is due you to planar two aromatic rings (like >> biphenyl). >> Should I ignore it and go on? >> Any kind of help would be appreciated. >> Thanks in advance >> W. Flak >> >> >> > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > ____________________ Robert V. Kolakowski, Ph. D. Post Doc, K. C. Nicolaou Lab The Scripps Research Institute La Jolla, CA 92037 Laboratory Tel. 858.784.2480 From owner-chemistry@ccl.net Sat May 22 22:53:00 2010 From: "Cristina Aparecida Barboza crissetubal(!)gmail.com" To: CCL Subject: CCL:G: Negative Frequency Message-Id: <-41921-100522132104-23238-2I38GdkHabJumuhrOs1j7A-x-server.ccl.net> X-Original-From: Cristina Aparecida Barboza Content-Type: multipart/alternative; boundary=0016e65a09469ed826048732070d Date: Sat, 22 May 2010 17:20:52 +0000 MIME-Version: 1.0 Sent to CCL by: Cristina Aparecida Barboza [crissetubal^-^gmail.com] --0016e65a09469ed826048732070d Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear William Flak, I heard the same before, that small negative frequencies can be ignored, bu= t I think that -50 or -19 cm-1 are too high to be neglected. A small frequenc= y would be less than 2 cm-1. You should try to do a preoptimization with a semiempirical method as PM6 in Gaussian or Mopac then to do your optimization with B3LYP/6-311++G** or B3LYP/6-31G*. Best regards --=20 M.Sc. Cristina Aparecida Barboza ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Doctorado en Fisicoqu=EDmica Molecular, Facultad de Ecolog=EDa y Recursos Naturales, Universidad Andr=E9s Bello - UNAB, Santiago, Chile Laboratorio de Quimica Teorica, Facultad de Quimica y Biologia, Universidad de Santiago de Chile - USACH, Santiago, Chile --0016e65a09469ed826048732070d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear William Flak,

I heard the same before, that small negative freq= uencies can be ignored, but I think that -50 or -19 cm-1 are too high to be= neglected. A small frequency would be less than 2 cm-1. You should try to = do a preoptimization with a semiempirical method as PM6 in Gaussian or Mopa= c then to do your optimization with B3LYP/6-311++G** or B3LYP/6-31G*.

Best regards

--
M.Sc. Cristina Aparecida Barboza
~~~~~~~~= ~~~~~~~~~~~~~~~~~~~~~~~
Doctorado en Fisicoqu=EDmica Molecular,
Facu= ltad de Ecolog=EDa y Recursos Naturales,
Universidad Andr=E9s Bello - UN= AB,
Santiago, Chile

Laboratorio de Quimica Teorica,
Facultad de Quimi= ca y Biologia,
Universidad de Santiago de Chile - USACH,
Santiago, Ch= ile
--0016e65a09469ed826048732070d--
You can try the following:
Distort the mol= ecule along the arrow of the  mode which is giving negative frequency.=
Then reoptimize.
 regards.
Partha.


--- On Sat,= 22/5/10, W. Flak williamflak*|*yahoo.com <owner-chemistry(a)ccl.net>= ; wrote:

From: W. Flak williamflak*= |*yahoo.com <owner-chemistry(a)ccl.net>
Subject: CCL: Negative Frequ= ency
To: "Kundu, Partha Pratim " <partha1kundu(a)yahoo.com><= br>Date: Saturday, 22 May, 2010, 9:47 PM

Sent to CCL by: "W.  Flak" [williamflak^^yahoo.com]
Dear CCL
I= have optimized my molecule using B3LYP/6-311++G**, during freq step I got = -50
negative frequency.
The same job has been optimized basing on B3LYP/6-31G* and gave me a negative
frequency at -19
I remember I r= ead a paper/book saying this low frequencies could be ignored. Is
that = right?
This negative frequency is due you to planar two aromatic rings (= like
biphenyl).
Should I ignore it and go on?
Any kind of help wo= uld be appreciated.
Thanks in advance
W. Flak



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