From owner-chemistry@ccl.net Thu Nov 21 06:48:00 2013 From: "Jeya Vimalan jeyavimalan2k^^^gmail.com" To: CCL Subject: CCL: power spectrum Message-Id: <-49353-131121064605-27645-NQqOexXrVhkSOhmGQn1dzw#,#server.ccl.net> X-Original-From: Jeya Vimalan Content-Type: multipart/alternative; boundary=bcaec5101cbbd573ea04ebae7030 Date: Thu, 21 Nov 2013 12:45:56 +0100 MIME-Version: 1.0 Sent to CCL by: Jeya Vimalan [jeyavimalan2k!^!gmail.com] --bcaec5101cbbd573ea04ebae7030 Content-Type: text/plain; charset=ISO-8859-1 dear all, does any one know how one can extract power spectrum > from a trajectory from a vasp md simulation. if there exists any scripts can you please share it with me. best regards, vimal --bcaec5101cbbd573ea04ebae7030 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
dear all,
does any one know how one can extract power = spectrum
from a trajectory from a vasp md simulation.=A0
if there exists any scripts can you please share it with me.
be= st regards,
vimal

--bcaec5101cbbd573ea04ebae7030-- From owner-chemistry@ccl.net Thu Nov 21 08:04:00 2013 From: "Radhika Narayanan radhikanarayananbdu-,-gmail.com" To: CCL Subject: CCL: How to measure the stability of transition metal complexes Message-Id: <-49354-131121051314-20168-qA9v7MuNM4xnCzcTXoRekQ.:.server.ccl.net> X-Original-From: "Radhika Narayanan" Date: Thu, 21 Nov 2013 05:13:13 -0500 Sent to CCL by: "Radhika Narayanan" [radhikanarayananbdu=gmail.com] Dear all, I am doing some work on transition metal complexes.I would like to know, how to measure the stability of transition metal complex using computational techniques. Thanks in advance. Sincerely, Radhika From owner-chemistry@ccl.net Thu Nov 21 09:37:00 2013 From: "Laidig, Bill laidig.wd]*[pg.com" To: CCL Subject: CCL: Recommendation for QMD Review Message-Id: <-49355-131121093527-21692-ndv3qeih0h67/N+8t+b8AA_._server.ccl.net> X-Original-From: "Laidig, Bill" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Thu, 21 Nov 2013 14:35:17 +0000 MIME-Version: 1.0 Sent to CCL by: "Laidig, Bill" [laidig.wd * pg.com] Hi, Last week, I asked for a recommendation spelled out below. I got several useful replies. One I want to share is a great book that is relatively new (2009 for hardcover) and covers a lot of what I was asking: Ab Initio Molecular Dynamics Dominik Marx & Jürg Hutter I got the Kindle edition for $34 (paperback $68). Bill -----Original Message----- > From: owner-chemistry+laidig.wd==pg.com|a|ccl.net [mailto:owner-chemistry+laidig.wd==pg.com|a|ccl.net] On Behalf Of Laidig, Bill laidig.wd]=[pg.com Sent: Wednesday, November 13, 2013 3:03 PM To: Laidig, Bill Subject: CCL: Recommendation for QMD Review Sent to CCL by: "Laidig, Bill" [laidig.wd-.-pg.com] Hi, I am currently trying to decide what QMD program(s) to advocate for our modeling group and am looking for a review(s) of the current state-of-the-art in terms of: 1) Theory (what methodologies are in use, best practices, frontiers, areas of agreement/disagreement); 2) Programs (speed, scaling behavior in CPUs/GPUs, ease of use, analysis abilities, cost...); 3) Simulations (practical limits in box size, atoms number, element types, addition of constraints/pathways...) Most of what I have found is either too specific or biased. By the way, what I mean by QMD is Born-Oppenheimer dynamics (classical nuclei with QM electrons), either CP or PAW based. I am leaning toward Abinit (scales well, free) or VASP (fast, not free), but am pretty open to other suggestions. I am a traditional quantum chemist by training and have a lot of classical protein simulation experience as well, but not very knowledgable about plane wave simulations. I really want to find out what folks are using now and the computational cost in CPU hrs. for systems as a function of box size and simulation length. Thanks, Bill Bill Laidig BRTC-BRB 8611 Becket Rd West Chester, OH 45069-7053http://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 Thu Nov 21 10:14:00 2013 From: "Jim Kress ccl_nospam^^^kressworks.com" To: CCL Subject: CCL: power spectrum Message-Id: <-49356-131121094851-26848-biH/79e7en1uwlNl2OIuVw++server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0177_01CEE69E.D6C63BE0" Date: Thu, 21 Nov 2013 09:48:31 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam-x-kressworks.com] This is a multipart message in MIME format. ------=_NextPart_000_0177_01CEE69E.D6C63BE0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Any particular reason you don't ask your question at the VASP support forum? http://cms.mpi.univie.ac.at/vasp-forum/forum.php Jim > From: owner-chemistry+ccl_nospam==kressworks.com,ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com,ccl.net] On Behalf Of Jeya Vimalan jeyavimalan2k^^^gmail.com Sent: Thursday, November 21, 2013 6:46 AM To: Kress, Jim Subject: CCL: power spectrum dear all, does any one know how one can extract power spectrum > from a trajectory from a vasp md simulation. if there exists any scripts can you please share it with me. best regards, vimal ------=_NextPart_000_0177_01CEE69E.D6C63BE0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

 

Any particular reason you don’t ask your question at the VASP = support forum?

http://cms.mpi.= univie.ac.at/vasp-forum/forum.php

 

Jim

 

From: = owner-chemistry+ccl_nospam=3D=3Dkressworks.com,ccl.net = [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com,ccl.net] On = Behalf Of Jeya Vimalan jeyavimalan2k^^^gmail.com
Sent: = Thursday, November 21, 2013 6:46 AM
To: Kress, Jim =
Subject: CCL: power spectrum

 

dear = all,

does any one know how one = can extract power spectrum

from a trajectory from a vasp md = simulation. 

if there = exists any scripts can you please share it with = me.

best = regards,

vimal

 

------=_NextPart_000_0177_01CEE69E.D6C63BE0-- From owner-chemistry@ccl.net Thu Nov 21 18:41:00 2013 From: "Frank Neese Frank.Neese]![cec.mpg.de" To: CCL Subject: CCL: ORCA 3.0.1 released Message-Id: <-49357-131121155754-20066-EM1GEjDfj4PfCJCVOoWgFA#server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-15"; format=flowed Date: Thu, 21 Nov 2013 21:57:41 +0100 MIME-Version: 1.0 Sent to CCL by: Frank Neese [Frank.Neese ~ cec.mpg.de] Dear CCLers, we are happy to announce the release of the ORCA program suite version 3.0.1. ORCA is a versatile and efficient electronic structure program that is free of charge for academic users. The present minor release mostly fixes some minor problems that became apparent after releasing version 3.0.0 a few weeks ago. However, a few new features made it into the release: - EOM (parallel, InCore, OnDisk, improved convergence) - SCF-Hessian (IR Intensities) - NBO interface (NBO5 or NBO6 via environment variable) - NumGeo (Keyword for numerical Hessian in OPT-runs using (Re)Calc_Hessian) - Translation-invariance for numerical gradients - TPrint now works with CIS We are welcoming new users and very much hope that with that minor release the program will be even more useful for our fast growing user base. As always, if you use the program and appreciate our efforts, we kindly ask for citations to our original papers. This will allow us to keep going and remain free of charge for the academic user community. You can download ORCA at http://www.cec.mpg.de/downloads.html We have an active forum where users can ask questions or discuss features. Enjoy the program! Frank Neese on behalf of the ORCA Development Team -- ------------------------------------------------------------------------- Prof. Dr. Frank Neese - Director - Max-Planck Institute for Chemical Energy Conversion Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany E-Mail: Frank.Neese-x-cec.mpg.de ------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Nov 21 19:16:00 2013 From: "Antonio G. De Crisci antonio.decrisci]^[nrcan.gc.ca" To: CCL Subject: CCL: Running Gaussian 09 on Ubuntu 12.04 (or earlier) Message-Id: <-49358-131121165740-23954-TlvjoS31L143hi97Y8/JiA..server.ccl.net> X-Original-From: "Antonio G. De Crisci" Date: Thu, 21 Nov 2013 16:57:39 -0500 Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci^^nrcan.gc.ca] Hello, Was curious if any of you run G09 and GV5 on Ubuntu and if there are any problems? This would be the 64-bit multiprocessor version. Thanks, Anthony From owner-chemistry@ccl.net Thu Nov 21 19:51:00 2013 From: "Oellien, F (Frank) frank.oellien[]msd.de" To: CCL Subject: CCL: Call For Paper - 10. International Conference on Chemical Structures and 10. German Conference on Chemoinformatics Message-Id: <-49359-131121174210-26944-MnPY/Jhf2STiXIsAFjJ1Hg:server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-Type: multipart/mixed; boundary="===============2147260628==" Date: Thu, 21 Nov 2013 23:41:58 +0100 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien##msd.de] --===============2147260628== Content-Language: en-US Content-Type: multipart/related; boundary="_004_00FE5FB90A64044BA1B6542C213F3F05011F1537860CBEBRMXP5100_"; type="multipart/alternative" --_004_00FE5FB90A64044BA1B6542C213F3F05011F1537860CBEBRMXP5100_ Content-Type: multipart/alternative; boundary="_000_00FE5FB90A64044BA1B6542C213F3F05011F1537860CBEBRMXP5100_" --_000_00FE5FB90A64044BA1B6542C213F3F05011F1537860CBEBRMXP5100_ Content-Type: text/plain; charset="us-ascii" C A L L F O R P A P E R S 10th International Conference on Chemical Structures and 10th German Conference on Chemoinformatics NH Leeuwenhorst Conference Hotel, Noordwijkerhout, The Netherlands 1-5 June 2014 Visit the conference website at www.int-conf-chem-structures.org for more information. The 10th International Conference on Chemical Structures (ICCS) and the 10th German Conference on Chemoinformatics (GCC) are teaming up for their 2014 conferences. Building on past successes of both conference series the 2014 event will offer a strong scientific program covering all aspects of cheminformatics and molecular modeling. For this joint event, the ICCS/GCC is seeking presentations of novel research and emerging technologies for the following plenary sessions: o Cheminformatics > advances in structure representation > molecular similarity and diversity > chemical information visualization > reaction handling and electronic lab notebooks (ELNs) o Structure-Activity and Structure-Property Prediction > industrialized and large-scale model building > multi-objective optimization and multi-property prediction > assessment of uncertainties in predictive modeling > graphical methods for SAR analysis o Structure-Based Drug Design and Virtual Screening > improved understanding of protein-ligand interactions > modeling of protein-protein interactions (PPIs) > modeling of challenging targets > advances in antibody modeling o Analysis of Large Chemistry Spaces > design, profiling and comparison of compound collections and screening sets > machine learning and knowledge extraction from databases > improved visualization of disparate data types > mining of chemical literature and patents o Integration of Chemical Information with other Resources > advances in chemogenomics > integration of medical and biological information with chemical information > semantic technologies as a driving force of integration > chemical information using mobile technologies and social media o Dealing with Biological Complexity > analysis and prediction of poly-pharmacology > analysis of high-content screening data > pathways and biological networks > druggability of targets We also welcome contributions in any aspect of the computer handling of chemical structure information, such as: automatic structure elucidation, computer-aided synthesis planning, combinatorial chemistry and diversity analysis, web technology and its effect on chemical information, electronic publishing, MM or QM/MM simulations, practical free energy calculations, modeling of ADME properties, material sciences, analysis and prediction of crystal structures, grid and cloud computing in cheminformatics. We encourage the submission of papers both on method and algorithm development as well as applications and case studies especially those demonstrating the predictive power of methods by experimental validation. > From the submissions the program committee and the scientific advisory board will select about 30 papers for the plenary sessions. All submissions that cannot be included in the plenary sessions will be automatically considered for the poster sessions. Before and after the official conference program free workshops will be offered by several companies including OpenEye (www.eyesopen.com) and the Chemical Computing Group (www.chemcomp.com). Joint Organizers: o Division of Chemical Information of the American Chemical Society (CINF) o Chemical Structure Association Trust (CSA Trust) o Division of Chemical Information and Computer Science of the Chemical Society of Japan (CSJ) o Chemistry-Information-Computer Division of the German Chemical Society (GDCh) o Royal Dutch Chemical Society (KNCV) o Chemical Information and Computer Applications Group of the Royal Society of Chemistry (RSC) o Swiss Chemical Society (SCS) Visit the conference website at www.int-conf-chem-structures.org for more information, including details on procedures for online abstract submission and conference registration. The deadline for the submission of abstracts is 31 January 2014. We hope to see you in Noordwijkerhout. Markus Wagener, ICCS Chair Frank Oellien, ICCS Co-Chair Uli Fechner, GCC Chair Dr. Frank Oellien Senior Scientist, Bioinformatics AH - Molecular Discovery Sciences MSD Animal Health Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien..msd.de Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.msd-animal-health.com [cid:image001.gif..01CEE713.42418C70] --_000_00FE5FB90A64044BA1B6542C213F3F05011F1537860CBEBRMXP5100_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

C A L L &nb= sp; F O R   P A P E R S

10th I= nternational Conference on Chemical Structures and

10th German Conference on Chemoinformatics

 

NH Leeuwenhorst C= onference Hotel, Noordwijkerhout, The Netherlands

1-5 June 2014

 

Visit the conference website at www.int-conf-chem-structures.org for= more information.

 

=

The 10th International Conference on Chemical Structur= es (ICCS) and the 10th German Conference on Chemoinformatics (GCC) are team= ing up for their 2014 conferences. Building on past successes of both confe= rence series the 2014 event will offer a strong scientific program covering= all aspects of cheminformatics and molecular modeling. For this joint even= t, the ICCS/GCC is seeking presentations of novel research and emerging tec= hnologies for the following plenary sessions:

 

   o Cheminformat= ics

      =   > advances in structure representation

        > molecular si= milarity and diversity

   = ;     > chemical information visualization

        > r= eaction handling and electronic lab notebooks (ELNs)

 

   o Struc= ture-Activity and Structure-Property Prediction    &nbs= p; 

     =    > industrialized and large-scale model building

        >= ; multi-objective optimization and multi-property prediction

        > = assessment of uncertainties in predictive modeling

        > graphical meth= ods for SAR analysis

 

   o Structure-Based Drug Design and Virtu= al Screening       

        > improv= ed understanding of protein-ligand interactions

        > modeling of protein= -protein interactions (PPIs)

  = ;      > modeling of challenging targets

        >= ; advances in antibody modeling

&nb= sp;

   o Analysis of Large Chemistr= y Spaces       

        > design, p= rofiling and comparison of compound collections and screening sets

        > = machine learning and knowledge extraction from databases

        > improved v= isualization of disparate data types

&nb= sp;       > mining of chemical literature = and patents

 

   o Integration of Chemical Information with other= Resources

     = ;   > advances in chemogenomics

        > integration of medical= and biological information with chemical information

        > semantic tech= nologies as a driving force of integration

        > chemical information usi= ng mobile technologies and social media

=  

   o Dealing with Biolo= gical Complexity

    = ;    > analysis and prediction of poly-pharmacology<= /o:p>

        &g= t; analysis of high-content screening data

        > pathways and biological = networks

     &= nbsp;  > druggability of targets

 

We also welcome contributions in= any aspect of the computer handling of chemical structure information, suc= h as: automatic structure elucidation, computer-aided synthesis planning, c= ombinatorial chemistry and diversity analysis, web technology and its effec= t on chemical information, electronic publishing, MM or QM/MM simulations, = practical free energy calculations, modeling of ADME properties, material s= ciences, analysis and prediction of crystal structures, grid and cloud comp= uting in cheminformatics.

 

We encourage the submission of papers both on m= ethod and algorithm development as well as applications and case studies es= pecially those demonstrating the predictive power of methods by experimenta= l validation.

 

From the submissions the program committee and the scientif= ic advisory board will select about 30 papers for the plenary sessions. All= submissions that cannot be included in the plenary sessions will be automa= tically considered for the poster sessions.

 

Before and after the official= conference program free workshops will be offered by several companies inc= luding OpenEye (www.eyesopen.com) and the Chemical Computing Group (www.chemcomp.com).

 

Joint Organizers:

   o Division of Chemical Inform= ation of the American Chemical Society (CINF)

   o Chemical Structure Association Trust (CSA Trust)<= /o:p>

   o Division of Chemical Informati= on and Computer Science of the Chemical Society of Japan (CSJ)

   o Chemistry-Information-Computer Divisi= on of the German Chemical Society (GDCh)

   o Royal Dutch Chemical Society (KNCV)

   o Chemical Information and Computer Applications = Group of the Royal Society of Chemistry (RSC)

   o Swiss Chemical Society (SCS)

 

Visit the conference we= bsite at www.int-conf-c= hem-structures.org for more information, including details on procedure= s for online abstract submission and conference registration.

 

The deadlin= e for the submission of abstracts is 31 January 2014.

 

We hope to see you = in Noordwijkerhout.

 

Markus Wagener, ICCS Chair

Frank Oellien, ICCS Co-Chair

Uli Fechner, GCC Chair

 

 

Dr. Frank Oellien

Senior Scientist, Bioinformatics

AH – Molecular Discove= ry Sciences

M= SD Animal Health Innovation GmbH

Zur Propstei

55270 Schwabenheim, Germany=

 

E-Mail: &nb= sp;    frank.oellien..msd.de

Phone:     +49 (6130) 948 365   &n= bsp;            = ;             <= o:p>

Fax: &nb= sp;       +49 (6130) 948 517   = ;            &n= bsp;            = ; 

Home=        http://www.msd-animal-h= ealth.com

3D"msd_ah_s=

 

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Hierzu geh=C3=B6ren folgende Vertriebsunternehmen: Humanarzneimittel: MSD Sharp & Dohme GmbH, Lindenplatz 1, 85540 Haar; HR M=C3=BCnchen B 6194 Gesch=C3=A4ftsf=C3=BChrer: Hanspeter Quodt (Vors.), Dr. Claus Dollinger, Dr= . Dr. Kristian L=C3=B6bner, Dr. Veit Stoll Aufsichtsratsvorsitzender: Dr. Axel Breitstadt Tierarzneimittel: Intervet Deutschland GmbH, Feldstr. 1a, 85716 Unterschlei=C3=9Fheim; HR M= =C3=BCnchen B 138151 Gesch=C3=A4ftsf=C3=BChrer: Dr. Daniel Sicher (Vors.), Christoph K=C3=B6lsch Weitere Unternehmen der deutschen MSD-Gruppe siehe http://info.msd.de/pflic= htangaben --===============1088596795== Content-Type: text/html; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable

Hinweis: Diese Email wird von einem Unternehmen der deutschen MSD-Gruppe= versandt. Hierzu geh=C3=B6ren folgende Vertriebsunternehmen:

Humanarzneimittel:

MSD Sharp & Dohme GmbH, Lindenplatz 1, 85540 Haar; HR M=C3=BCnchen B= 6194
Gesch=C3=A4ftsf=C3=BChrer: Hanspeter Quodt (Vors.), Dr. Claus Doll= inger,