From owner-chemistry@ccl.net Sun Feb 28 06:24:01 2016 From: "Rafael R. Pappalardo rafapa###us.es" To: CCL Subject: CCL: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52065-160228062130-31388-fmzZuN+0ToVi1dYFAsVp/A ~ server.ccl.net> X-Original-From: "Rafael R. Pappalardo" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Sun, 28 Feb 2016 12:21:16 +0100 MIME-Version: 1.0 Sent to CCL by: "Rafael R. Pappalardo" [rafapa[]us.es] My suggestion is to use scf=qc and integral=(grid=superfine). Best regards, Rafael --- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla (Spain) On 27/02/2016 06:03, Bulumoni Kalita bulumoni() dibru.ac.in wrote: > Sent to CCL by: "Bulumoni Kalita" [bulumoni|-|dibru.ac.in] > Dear Users, > Thank you very much for your replies. The error shows as > > "Convergence failure -- run terminated" > > The input is as follows > > %chk=Pd4_3.chk > # opt(maxcycle=500) um06l/genecp nosym > > Pd4 > > 0 1 > Pd 1.55076100 -0.20840900 -0.52663500 > Pd -0.96047300 -1.23708300 -0.51996300 > Pd 0.00639500 -0.00412900 1.56159200 > Pd -0.59668400 1.44962100 -0.51499300 > > Pd 0 > LANL2DZ > **** > > Pd 0 > LANL2DZ > > Freezing one atom also did not solve the problem. > > Look forward for your discussion.> To recover the email address of the author of the message, please > change From owner-chemistry@ccl.net Sun Feb 28 10:14:01 2016 From: "Roland Lindh roland.lindh|-|kemi.uu.se" To: CCL Subject: CCL: 8th MQM conference Message-Id: <-52066-160228092326-21943-UO+uy+GPj+dHzkThe7sgEw===server.ccl.net> X-Original-From: "Roland Lindh" Date: Sun, 28 Feb 2016 09:23:25 -0500 Sent to CCL by: "Roland Lindh" [roland.lindh..kemi.uu.se] Welcome to The 8th Molecular Quantum Mechanics, June 26 - July 2016, Uppsala, Sweden Dear colleagues, It is with pleasure I invite you to attend the 8th Molecular Quantum Mechanics, June 26-July 1 2016 in Uppsala, Sweden. We hope that you will find the city of Uppsala and Uppsala University, founded in 1477, a worthy host of the symposium. The MQM 2016 will find inspiration from the academic excellence of Uppsala, as exemplified by local scientific giants as Carl von Linnaeus, Anders Celsius, and more recently the chemistry Nobel laureates The Svedberg and Arne Tiselius. The vicinity to Stockholm, closeness to Sweden's largest airport (Arlanda), the splendid nature of Uppland, with its soothing archipelago, and the inspirational Swedish summer we hope will be further reasons for you to come and visit us in June 2016. Scientific program The scientific programme will feature the very best of speakers from all over the world. You will find the latest programme updates on the symposium website. www.akademikonferens.uu.se/mqm2016 Abstract submission-now open! Submission of abstracts should be made as soon as possible, but no later than March 23. The abstract should be entered on-line by using the abstract submission form Visit the symposium website for more information and abstract guidelines: Register before March 2 Register before March 2 and take advantage of the early-bird registration fee. You will find the link for registration here. Please read the registration guidelines on the symposium website before registering: http://www-conference.slu.se/mqm2016/registration.html Social programme Find out more about Uppsala! The social program offers a variety of excursions, choose between a visit in Linnaeus summerhouse and gardens, a nice boat trip or a guided tour in an elk park. Do not miss the conference dinner on Thursday, June 30, in a typical Uppsala student-like atmosphere. Further information to found on the website. Contact If you have any questions, please contact the Conference secretariat:- Academic Conferences - Tel. +46 18 67 15 39, +46 18 67 10 03 - Fax. +46 18 67 35 30 - E-mail mqm2016**akademikonferens.uu.se Important dates Early bird fee deadline: March 2, 2016 Abstract submission deadline: March 23, 2016 Notification of abstract acceptance: April 25, 2016 Normal registration fee deadline: May 4, 2016 If you should have received this email twice, we are sorry for the inconvenience. This email was sent to several email lists, and your email address may have been on more than one list. Very welcome to Uppsala in June 2016! Prof. Roland Lindh, Chair of MQM 2016 Academic Conferences - universities in cooperation: Karolinska Institutet, SLU & Uppsala University www.akademikonferens.uu.se/mqm2016| +46 18 67 15 27 or +46 18 67 10 03 | mqm2016**akademikonferens.uu.se From owner-chemistry@ccl.net Sun Feb 28 10:48:01 2016 From: "John McKelvey jmmckel-*-gmail.com" To: CCL Subject: CCL: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52067-160228101834-14338-N+VUxF7tiQkQYi11YMx0+A,,server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=089e0115fca0559c01052cd60b3e Date: Sun, 28 Feb 2016 09:18:28 -0600 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel*gmail.com] --089e0115fca0559c01052cd60b3e Content-Type: text/plain; charset=UTF-8 Is it possible in G09 to "smear" the density near the homo-lumo gap? John McKelvey On Sun, Feb 28, 2016 at 5:21 AM, Rafael R. Pappalardo rafapa###us.es < owner-chemistry[a]ccl.net> wrote: > > Sent to CCL by: "Rafael R. Pappalardo" [rafapa[]us.es] > My suggestion is to use scf=qc and integral=(grid=superfine). > > Best regards, > Rafael > > --- > Dr. Rafael R. Pappalardo > Dept. Quimica Fisica, Fac. de Quimica, > Univ. de Sevilla (Spain) > > On 27/02/2016 06:03, Bulumoni Kalita bulumoni() dibru.ac.in wrote: > >> Sent to CCL by: "Bulumoni Kalita" [bulumoni|-|dibru.ac.in] >> Dear Users, >> Thank you very much for your replies. The error shows as >> >> "Convergence failure -- run terminated" >> >> The input is as follows >> >> %chk=Pd4_3.chk >> # opt(maxcycle=500) um06l/genecp nosym >> >> Pd4 >> >> 0 1 >> Pd 1.55076100 -0.20840900 -0.52663500 >> Pd -0.96047300 -1.23708300 -0.51996300 >> Pd 0.00639500 -0.00412900 1.56159200 >> Pd -0.59668400 1.44962100 -0.51499300 >> >> Pd 0 >> LANL2DZ >> **** >> >> Pd 0 >> LANL2DZ >> >> Freezing one atom also did not solve the problem. >> >> Look forward for your discussion.> To recover the email address of the >> author of the message, please changehttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- John McKelvey 545 Legacy Pointe Dr O'Fallon, MO 63376 636-294-5203 jmmckel[a]gmail.com --089e0115fca0559c01052cd60b3e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Is it possible in G09 to "smear" the densit= y near the homo-lumo gap?

John McKelvey

On Sun, Feb 28, 2016 at 5:21 A= M, Rafael R. Pappalardo rafapa###us.es <owner-chemistry[a]ccl.net> wrote:

Sent to CCL by: "Rafael R. Pappalardo" [rafapa[]us.es]
My suggestion is to use scf=3Dqc and integral=3D(grid=3Dsuperfine).

Best regards,
Rafael

---
Dr. Rafael R. Pappalardo
Dept. Quimica Fisica, Fac. de Quimica,
Univ. de Sevilla (Spain)

On 27/02/2016 06:03, Bulumoni Kalita bulumoni() dibru.ac.in wrote:
Sent to CCL by: "Bulumoni=C2=A0 Kalita" [bulumoni|-|dibru.ac.in]
Dear Users,
=C2=A0 =C2=A0 Thank you very much for your replies.=C2=A0 The error shows a= s

"Convergence failure -- run terminated"

The input is as follows

%chk=3DPd4_3.chk
# opt(maxcycle=3D500) um06l/genecp nosym

Pd4

0 1
Pd=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.55076100=C2=A0 =C2=A0-= 0.20840900=C2=A0 =C2=A0-0.52663500
Pd=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0-0.96047300=C2=A0 =C2=A0-= 1.23708300=C2=A0 =C2=A0-0.51996300
Pd=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.00639500=C2=A0 =C2=A0-= 0.00412900=C2=A0 =C2=A0 1.56159200
Pd=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0-0.59668400=C2=A0 =C2=A0 = 1.44962100=C2=A0 =C2=A0-0.51499300

Pd 0
LANL2DZ
****

Pd 0
LANL2DZ

Freezing one atom also did not solve the problem.

Look forward for your discussion.> To recover the email address of the a= uthor of the message, please change


-=3D This is automatically added to each message by the mailing script =3D-=
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--
John McKelvey
545 Le= gacy Pointe Dr
O'Fallon, MO 63376
636-294-5203
jmmckel[a]gmail.com
=
--089e0115fca0559c01052cd60b3e-- From owner-chemistry@ccl.net Sun Feb 28 19:12:01 2016 From: "Fedor Goumans goumans^^^scm.com" To: CCL Subject: CCL:G: DFT, Broken-symmetry on MOF Message-Id: <-52068-160228171056-25892-5vS6KWq4jxHSy5grIG7/Bg|server.ccl.net> X-Original-From: Fedor Goumans Content-Type: multipart/alternative; boundary="------------070403070207020707010200" Date: Sun, 28 Feb 2016 23:10:50 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans..scm.com] This is a multi-part message in MIME format. --------------070403070207020707010200 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Dear Vijay, Do you want to run under periodic boundary conditions? With BAND you can select which atoms to spin-flip, just as you can for ADF. Compare this teaching example for BAND: http://www.scm.com/Doc/Teaching/SpinDensityAntiFerromagneticIron.html with the ADF tutorial on spin coupling in Fe4S4: http://www.scm.com/Doc/Doc2014/GUI/GUI_tutorial/page88.html Whether you need to create a supercell depends on your unit cell and how you want to distribute your spins. Best wishes, Fedor On 26-2-2016 16:27, Vijay Singh Parmar vsparmar(_)iiserb.ac.in wrote: > Respected computational chemists, > > I am a beginner at computational chemistry. > > I want to perform a broken-symmetry calculation in order to find the > exchange interactions in my Dy-MOF(metal-organic frameworks) Using > gaussian09 or ORCA or ADF. I tried for a Di-nuclear complex but i dont > get how to do the same for a MOF, should i use the assymetric unit > only or more number of atoms somehow? > > please help! Thanks in advance > > > Vijay Singh Parmar > Department of Chemistry > Contact: +91-9691888500 > IISER Bhopal > Bhouri -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 https://www.scm.com https://twitter.com/SCM_Amsterdam https://www.linkedin.com/company/scientific-computing-&-modelling-nv --------------070403070207020707010200 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Dear Vijay,

Do you want to run under periodic boundary conditions? With BAND you can select which atoms to spin-flip, just as you can for ADF.

Compare this teaching example for BAND:
http://www.scm.com/Doc/Teaching/SpinDensityAntiFerromagneticIron.html
with the ADF tutorial on spin coupling in Fe4S4:
http://www.scm.com/Doc/Doc2014/GUI/GUI_tutorial/page88.html

Whether you need to create a supercell depends on your unit cell and how you want to distribute your spins.

Best wishes,
Fedor

On 26-2-2016 16:27, Vijay Singh Parmar vsparmar(_)iiserb.ac.in wrote:
Respected computational chemists,

I am a beginner at computational chemistry.
 
I want to perform a broken-symmetry calculation in order to find the exchange interactions in my Dy-MOF(metal-organic frameworks) Using gaussian09 or ORCA or ADF. I tried for a Di-nuclear complex but i dont get how to do the same for a MOF, should i use the assymetric unit only or more number of atoms somehow?

please help! Thanks in advance


Vijay Singh Parmar
Department of Chemistry 
Contact: +91-9691888500
IISER Bhopal
Bhouri

-- 
Dr. T. P. M. (Fedor) Goumans
Business Developer
Scientific Computing & Modelling NV (SCM)
Vrije Universiteit, FEW, Theoretical Chemistry
De Boelelaan 1083
1081 HV Amsterdam, The Netherlands
T +31 20 598 7625
https://www.scm.com
https://twitter.com/SCM_Amsterdam
https://www.linkedin.com/company/scientific-computing-&-modelling-nv
--------------070403070207020707010200-- From owner-chemistry@ccl.net Sun Feb 28 19:49:01 2016 From: "Flavio Ballante ballantef_._biochem.wustl.edu" To: CCL Subject: CCL: Structure-Based drug design: Clusterizer-DockAccessor 1.0 Message-Id: <-52069-160228193301-9463-x0kS9c/TtOZFzZzfu5sQeg__server.ccl.net> X-Original-From: "Flavio Ballante" Date: Sun, 28 Feb 2016 19:33:00 -0500 Sent to CCL by: "Flavio Ballante" [ballantef]![biochem.wustl.edu] Dear all - Recently a methodology for binding pose selection and docking assessment in structure-based drug design has been published by our group (http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00603). This methodology is called: Clusterizer-DockAccessor. Briefly, Clusterizer: Performs a complete cluster analysis and extrapolates best docked (BD), best cluster (BC) and best fit (BF) poses by using three different RMSD metrics (the standard heavy-atom RMSD (s), the Hungarian symmetry-corrected heavy-atom RMSD (h) and the minimum-distance heavy-atom RMSD (m)). Clusterizer releases results with a standard output readable by DockAccessor. Moreover, Clusterizer can be used to extrapolate BD and BC poses when docking novel/untested compounds. DockAccessor: Reads the Clusterizers results and calculates the docking accuracy. We are pleased to inform you that the software and the documentation (user manual and tutorial) are freely available from http://cheminf.com/ and http://cmd.wustl.edu/. We hope you find Clusterizer-DockAccessor useful for your research, and welcome any feedback you may have. Sincerely, Flavio Ballante -- Dr. Flavio Ballante Biochemistry & Molecular Biophysics Washington University School of Medicine 660 S. Euclid Ave. Saint Louis, MO 63110 United States Lab. Phone: 314-747-5169 E-mail: ballantef++biochem.wustl.edu