From owner-chemistry@ccl.net Tue Jul 3 11:18:00 2012 From: "Marcel Swart marcel.swart- -icrea.cat" To: CCL Subject: CCL: CECAM Workshop on Spin States Message-Id: <-47165-120703091613-8708-2Hv3/C18EXt/SK4uSNeBIQ%x%server.ccl.net> X-Original-From: "Marcel Swart" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Tue, 3 Jul 2012 15:16:00 +0200 MIME-Version: 1.0 Sent to CCL by: "Marcel Swart" [marcel.swart%a%icrea.cat] Dear all, We are organizing a scientific workshop on “Spin states in biochemistry and inorganic chemistry”, to be held at the Z-Cam center in Zaragoza, Spain from 18-21 September 2012. The workshop is part of the renowned CECAM series of workshops. CECAM (Centre Européen de Calcul Atomique et Moléculaire) is a European organization devoted to the promotion of fundamental research on advanced computational methods and to their application to important problems in frontier areas of science and technology. Elucidating the role and effect of different spin states on catalysis, even deciding which spin-state occurs naturally, is presently one of the most challenging endeavors both > from an experimental and theoretical point-of-view. This workshop will bring together theoretical and experimental experts to discuss this situation and propose best practices on how to deal with the problem in future scientific research. The list of renowned experts includes: J. Harvey (Bristol), M. Kaupp (Berlin), E. Münck (Carnegie-Mellon), L. Que Jr. (Minnesota), J.P. Perdew (New Orleans), P. Siegbahn (Stockholm), W. Thiel (MPI-Mülheim), among others. The full list of participants and speakers is given at: http://www.cecam.org/workshop-0-671.html There are a limited number of places available to attend this workshop and present your work, so please send us a message with a tentative title of your talk. The deadline for it is: 23 July. Marcel Swart Mikael Johansson (organizers) =================================== dr. Marcel Swart ICREA Research Professor at Institut de Química Computacional Universitat de Girona Parc Científic i Tecnològic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart^-^icrea.cat marcel.swart^-^udg.edu web http://www.marcelswart.eu =================================== From owner-chemistry@ccl.net Tue Jul 3 14:35:00 2012 From: "Joe Corkery jcorkery*_*eyesopen.com" To: CCL Subject: CCL: Congratulations to the winners of the OpenEye Outstanding Junior Faculty Award Message-Id: <-47166-120703110031-10743-ae/6tO0PX5kVwkFNoljqxg*_*server.ccl.net> X-Original-From: Joe Corkery Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_CC18813D1720Cjcorkeryeyesopencom_" Date: Tue, 3 Jul 2012 08:00:13 -0700 MIME-Version: 1.0 Sent to CCL by: Joe Corkery [jcorkery_-_eyesopen.com] --_000_CC18813D1720Cjcorkeryeyesopencom_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable OpenEye Scientific Software is pleased to announce and congratulate the win= ners of the OpenEye Outstanding Junior Faculty Award. Recipients will be pr= esented with their award certificate and $1,000 cash prize during the Fall = 2012 ACS COMP division poster session on August 21, 2012 in Philadelphia. The Outstanding Junior Faculty are: * Gregory Beran University of California, Riverside Practical prediction of molecular crystal structures and properties from fi= rst principles * Jerome Delhommelle University of No= rth Dakota Unraveling the mechanisms of crystal nucleation and growth at the nanoscale * Michael Shirts = University of Virginia New methods for thermodynamic analysis and sampling of molecular simulation= s * Yaroslava Yingling North Car= olina State University Tuning DNA structural bending with charged nanoparticles About the OpenEye Outstanding Junior Faculty Award The OpenEye Outstanding Junior Faculty Award is designed to recognize the w= ork of and assist rising new faculty members in gaining visibility within t= he COMP community. The Award is granted semi-annually at the ACS National M= eetings. About OpenEye Scientific Software OpenEye Scientific Software Inc. is a privately held company headquartered = in Santa Fe, New Mexico, with offices in Boston, Massachusetts, Strasbourg,= France and Tokyo, Japan. It was founded in 1997 to develop large-scale mol= ecular modeling applications and toolkits. Primarily aimed towards drug dis= covery and design, areas of application include: * chemical informatics * structure generation * shape comparison * docking * fragment replacement * electrostatics * crystallography * visualization The software is designed for scientific rigor, as well as speed, scalabilit= y and platform independence. OpenEye makes most of its technology available= as toolkits - programming libraries suitable for custom development. OpenE= ye software typically is distributable across multiple processors, supports= 64-bit processing, and runs on Linux, Windows and Mac OS X. For further in= formation on the company and its products, see www.eyesopen.com For additional information Joseph Corkery, M.D. Vice President, Business Development +1-505-473-7385 x76 Email: business:_:eyesopen.com --_000_CC18813D1720Cjcorkeryeyesopencom_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
OpenEye Sci= entific Software is pleased to announce and congratulate the wi= nners of the OpenEye Outstanding Junior Faculty Award. Recipients will be p= resented with their award certificate and $1,000 cash prize during the Fall= 2012 ACS COMP division poster session on August 21, 2012 in Philadelphia.<= /span>

The Outstanding Junior Faculty are:

    =
  • Gregory Beran University of Ca= lifornia, Riverside
    Practical prediction of molecular crystal structu= res and properties from first principles

  • Jerome Delhommelle University = of North Dakota
    Unraveling the mechanisms of crystal nucleation and g= rowth at the nanoscale

  • Michael Shirts University of= Virginia
    New methods for thermodynamic analysis and sampling of mole= cular simulations

  • Yaroslava Yingling North Carolina State Univer= sity
    Tuning DNA structural bending with charged nanoparticles

The = OpenEye Outstanding Junior Faculty Award is designed to recognize the work = of and assist rising new faculty members in gaining visibility within the C= OMP community. The Award is granted semi-annually at the ACS National Meeti= ngs.

About OpenEye Scientific Software

OpenEye Scientific = Software Inc. is a privately held company headquartered in Santa Fe, New Me= xico, with offices in Boston, Massachusetts, Strasbourg, France and Tokyo, = Japan. It was founded in 1997 to develop large-scale molecular modeling app= lications and toolkits. Primarily aimed towards drug discovery and design, = areas of application include:

The software is designed for scientific ri= gor, as well as speed, scalability and platform independence. OpenEye makes= most of its technology available as toolkits - programming libraries suita= ble for custom development. OpenEye software typically is distributable acr= oss multiple processors, supports 64-bit processing, and runs on Linux, Win= dows and Mac OS X. For further information on the company and its products,= see www.eyesopen.com

For additional information
Joseph= Corkery, M.D.
Vice President, Business Development
+1-505-473-7385 x= 76
Email: business:_:eyesopen.com=

--_000_CC18813D1720Cjcorkeryeyesopencom_-- From owner-chemistry@ccl.net Tue Jul 3 15:30:00 2012 From: "Ramachandran Chelat rcchelat|gmail.com" To: CCL Subject: CCL: molecular orbitals using NWChem Message-Id: <-47167-120703143053-25115-d3nIV0Yg22fYFJjKtrB6kw!^!server.ccl.net> X-Original-From: "Ramachandran Chelat" Date: Tue, 3 Jul 2012 14:30:50 -0400 Sent to CCL by: "Ramachandran Chelat" [rcchelat a gmail.com] Dear CCL friends, Could you please explain how to plot the molecular orbitals using NWChem. I used the following input for O2 molecule: start M06L-O2 geometry O 0.000000 0.000000 0.000000 O 0.000000 0.000000 1.300000 end basis spherical O library STO-3g end scf vectors output O2.movecs end dplot TITLE HOMO vectors O2.movecs LimitXYZ -3.0 3.0 10 -3.0 3.0 10 -3.0 3.0 10 spin alpha orbitals view; 1;8 output homo.grd end task scf task dplot I have the .grd and .movecs files after the calculation. Which software (freely available) can plot the orbitals using these files? Thanks Ramachandran From owner-chemistry@ccl.net Tue Jul 3 16:06:01 2012 From: "Hao-Bo Guo guohaobo(_)gmail.com" To: CCL Subject: CCL:G: molecular orbitals using NWChem Message-Id: <-47168-120703160503-3728-72eM4X6LDugVaKI+PJ4vIg:_:server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=20cf3071c672ba526304c3f26d72 Date: Tue, 3 Jul 2012 16:04:57 -0400 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo-*-gmail.com] --20cf3071c672ba526304c3f26d72 Content-Type: text/plain; charset=ISO-8859-1 Hi Ramachandran, You can write the cube files, e.g., ###### # calculate the movecs file scf vectors output O2.movecs end # write cube files dplot TITLE HOMO vectors O2.movecs LimitXYZ -3.0 3.0 10 -3.0 3.0 10 -3.0 3.0 10 spin total # or alpha only as you did orbitals view; 1;8 output homo.cube end task scf task dplot ###### The Gaussian format cubes can then be visualized and plotted, e.g., with VMD. Hao-Bo Guo On Tue, Jul 3, 2012 at 2:30 PM, Ramachandran Chelat rcchelat|gmail.com < owner-chemistry:-:ccl.net> wrote: > > Sent to CCL by: "Ramachandran Chelat" [rcchelat a gmail.com] > Dear CCL friends, > Could you please explain how to plot the molecular orbitals using NWChem. > I used the following input for O2 molecule: > > start M06L-O2 > geometry > O 0.000000 0.000000 0.000000 > O 0.000000 0.000000 1.300000 > end > basis spherical > O library STO-3g > end > > scf > vectors output O2.movecs > end > > dplot > TITLE HOMO > vectors O2.movecs > LimitXYZ > -3.0 3.0 10 > -3.0 3.0 10 > -3.0 3.0 10 > spin alpha > orbitals view; 1;8 > output homo.grd > end > > task scf > task dplot > > I have the .grd and .movecs files after the calculation. Which software > (freely available) can plot the orbitals using these files? > > Thanks > Ramachandran> > > --20cf3071c672ba526304c3f26d72 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Ramachandran,
You can write the cube files, e.g.,
######
# calc= ulate the movecs file
scf
vectors output O2.movecs
end
# write cube files
dplot
=A0TITLE HOMO
=A0 vectors O2.movecs
=A0 LimitXYZ
=A0-3.0 3.0 10
=A0-3.0 3.0 10
=A0-3.0 3.0 10
=A0 spin total=A0 # or alpha only as you did
=A0 orbitals view; 1;8
=A0 output homo.cube
end
task scf
task dplot
######
The Gaussian format cubes can th= en be visualized and plotted, e.g., with VMD.

Hao-Bo Guo

On Tue, Jul 3, 2012 at 2:30 PM, Ramachandran Chelat = rcchelat|gmail.com <<= a href=3D"mailto:owner-chemistry:-:ccl.net" target=3D"_blank">owner-chemistry= :-:ccl.net> wrote:

Sent to CCL by: "Ramachandran =A0Chelat" [rcchelat a gmail.com]
Dear CCL friends,
Could you please explain how to plot the molecular orbitals using NWChem. I used the following input for O2 molecule:

start M06L-O2
geometry
O =A0 =A0 0.000000 =A0 =A0 0.000000 =A0 =A0 0.000000
O =A0 =A0 0.000000 =A0 =A0 0.000000 =A0 =A0 1.300000
end
basis spherical
=A0O library STO-3g
end

scf
vectors output O2.movecs
end

dplot
=A0TITLE HOMO
=A0 vectors O2.movecs
=A0 LimitXYZ
=A0-3.0 3.0 10
=A0-3.0 3.0 10
=A0-3.0 3.0 10
=A0 spin alpha
=A0 orbitals view; 1;8
=A0 output homo.grd
end

task scf
task dplot

I have the .grd and .movecs files after the calculation. =A0Which software = (freely available) can plot the orbitals using these files?

Thanks
Ramachandran



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