From owner-chemistry@ccl.net Fri Feb 15 05:01:00 2013 From: "Sergio Manzetti sergio.manzetti(a)gmx.com" To: CCL Subject: CCL: Method for calculating electron gas Message-Id: <-48230-130215045724-8836-2oP+AU+/QiXKvQgxckNMYA[#]server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary65371360922233305242" Date: Fri, 15 Feb 2013 10:57:12 +0100 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti]~[gmx.com] --========GMXBoundary65371360922233305242 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Dear all, is there a preferrable method in DFT to calculate the geometry and energy of the electron gas of a metallic structure? I have tried with PW91PW91, but there is a low rate of convergence. All the best Sergio --========GMXBoundary65371360922233305242 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear all= , is there a preferrable method in DFT to calculate the geometry and energy= of the electron gas of a metallic structure?

I have tried with = PW91PW91, but there is a low rate of convergence.

All the best
Sergio --========GMXBoundary65371360922233305242-- From owner-chemistry@ccl.net Fri Feb 15 10:05:00 2013 From: "Fedor Goumans goumans : scm.com" To: CCL Subject: CCL:G: Spin-orbit coupling to orbital-momentum Message-Id: <-48231-130215084145-11000-3UE551MwkRUeIjB+TLQleQ-.-server.ccl.net> X-Original-From: Fedor Goumans Content-Type: multipart/alternative; boundary="------------030909090500060404080707" Date: Fri, 15 Feb 2013 14:41:07 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans++scm.com] This is a multi-part message in MIME format. --------------030909090500060404080707 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Dear Sergio, Spin-orbit coupling can be included in both our molecular code ADF and our periodic code BAND, through the ZORA 2-component relativistic Hamiltonian. One can visualize the spin magnetization density of spin-orbit coupling calculations in ADFView, see our advanced tutorial: http://www.scm.com/Doc/Doc2012/GUI/GUI_tutorial/page118.html Visualization of these spinors is currently not possible for periodic structures. With kind regards, Fedor On 2/14/2013 5:15 PM, Sergio Manzetti sergio.manzetti+/-gmx.com wrote: > Dear all, is there a keyword in Gaussian, or is there any software > that can visualize or quantitize the spin-orbit coupling to the > orbital angular momentum in a rigid structure, such as a lattice? This > would naturally give valuable data for magnetic effects in a cluster > of atoms. > > Thanks > > Best wishes > > Sergio -- Dr. T. P. M. 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 F +31 20 598 7629 E-mail: goumans a scm.com http://www.scm.com --------------030909090500060404080707 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit

Dear Sergio,

Spin-orbit coupling can be included in both our molecular code ADF and our periodic code BAND, through the ZORA 2-component relativistic Hamiltonian.

One can visualize the spin magnetization density of spin-orbit coupling calculations in ADFView, see our advanced tutorial:
http://www.scm.com/Doc/Doc2012/GUI/GUI_tutorial/page118.html

Visualization of these spinors is currently not possible for periodic structures.

With kind regards,
Fedor

On 2/14/2013 5:15 PM, Sergio Manzetti sergio.manzetti+/-gmx.com wrote:

Dear all, is there a keyword in Gaussian, or is there any software that can visualize or quantitize the spin-orbit coupling to the orbital angular momentum in a rigid structure, such as a lattice? This would naturally give valuable data for magnetic effects in a cluster of atoms.

Thanks

Best wishes

Sergio

-- 
Dr. T. P. M. 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
F +31 20 598 7629
E-mail: goumans a scm.com
http://www.scm.com

--------------030909090500060404080707-- From owner-chemistry@ccl.net Fri Feb 15 10:40:00 2013 From: "Fedor Goumans goumans*o*scm.com" To: CCL Subject: CCL: Method for calculating electron gas Message-Id: <-48232-130215085635-11804-0NrimKqTNnRhLZi9CperXA%server.ccl.net> X-Original-From: Fedor Goumans Content-Type: multipart/alternative; boundary="------------010207020109090105060402" Date: Fri, 15 Feb 2013 14:55:57 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans]|[scm.com] This is a multi-part message in MIME format. --------------010207020109090105060402 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Dear Sergio, Metallic system can indeed be difficult to convergence. You could try: 1. a finite electron temperature (electron smearing) 2. a finer integration in k-space (if you're modeling a metal with PBC) 3. lower mixing values in your DIIS 4. alternative SCF algorithms to DIIS. Good luck, Fedor On 2/15/2013 10:57 AM, Sergio Manzetti sergio.manzetti(a)gmx.com wrote: > Dear all, is there a preferrable method in DFT to calculate the > geometry and energy of the electron gas of a metallic structure? > > I have tried with PW91PW91, but there is a low rate of convergence. > > All the best > > Sergio -- Dr. T. P. M. 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 F +31 20 598 7629 E-mail: goumans~!~scm.com http://www.scm.com --------------010207020109090105060402 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit

Dear Sergio,

Metallic system can indeed be difficult to convergence. You could try:
1. a finite electron temperature (electron smearing)
2. a finer integration in k-space (if you're modeling a metal with PBC)
3. lower mixing values in your DIIS
4. alternative SCF algorithms to DIIS.

Good luck,
Fedor

On 2/15/2013 10:57 AM, Sergio Manzetti sergio.manzetti(a)gmx.com wrote:

Dear all, is there a preferrable method in DFT to calculate the geometry and energy of the electron gas of a metallic structure?

I have tried with PW91PW91, but there is a low rate of convergence.

All the best

Sergio

-- 
Dr. T. P. M. 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
F +31 20 598 7629
E-mail: goumans~!~scm.com
http://www.scm.com

--------------010207020109090105060402-- From owner-chemistry@ccl.net Fri Feb 15 17:40:01 2013 From: "Shruthi Viswanath shruthi(0)ices.utexas.edu" To: CCL Subject: CCL: New server for protein docking Message-Id: <-48233-130215160344-936-LT+Jd5m5kGSRrjTm0A0feg+/-server.ccl.net> X-Original-From: "Shruthi Viswanath" Date: Fri, 15 Feb 2013 16:03:43 -0500 Sent to CCL by: "Shruthi Viswanath" [shruthi .. ices.utexas.edu] Hello everyone, We announce a new web server for docking protein complexes, DOCK/PIERR. It compares favorably to other leading automated docking packages available today. It is available free for public use at http://clsb.ices.utexas.edu/web/dock.html . No registration is required. Users receive the results of docking through email, which typically takes a few hours. Given the PDB structure of two proteins, the server returns the top ten structures of the complex formed by the two proteins. The docking algorithm is based on an initial Fast-Fourier Transform search using a coarse-grained residue level potential, followed by refinement using an atomic potential. The knowledge-based atomic and residue potentials used for ranking the models of complexes, are obtained by mathematical programming and provably optimal structural SVM algorithms. This involves exhaustive learning of potential parameters from hundreds of millions of inequalities generated from hundreds of thousands of models. You can find more details about the docking algorithm in the references below. References: 1) D V S Ravikant and Ron Elber, "PIE - Efficient filters and coarse grained potentials for unbound protein-protein docking", Proteins,78, 400-419 (2010). 2) D V S Ravikant and Ron Elber, "Energy design for protein-protein interactions", Journal of Chemical Physics, 135, 065102 (2011). 3) Shruthi Viswanath, D V S Ravikant and Ron Elber, "Improving ranking of models for protein complexes using side chain remodeling and atomic potentials", Proteins, in press (2013). Best regards Shruthi Viswanath