From owner-chemistry@ccl.net Thu Feb 20 03:53:00 2014 From: "Michel Petitjean petitjean.chiral(_)gmail.com" To: CCL Subject: CCL: Exercise for students (was: ICQC shame) Message-Id: <-49775-140220034951-25906-PPjiwcUKLGxX5BD/pmgNrQ::server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 20 Feb 2014 09:49:44 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral:+:gmail.com] Ok. You are right. Thank you. Apologies for having misinterpreted the claims seen there. The calculus can be updated with the corrected numbers. No doubt that the bias exists, and it is not specific to theoretical chemistry. It exists in other areas (and look at scientific committees, chairpersons, etc.). Progress was made, but there is still progress to come. Best regards. Michel. 2014-02-19 22:44 GMT+01:00 Susi Lehtola susi.lehtola]=[alumni.helsinki.fi : > > Sent to CCL by: Susi Lehtola [susi.lehtola^_^alumni.helsinki.fi] > On Wed, 19 Feb 2014 20:20:54 +0100 > ... > Please, lets stick to the facts. The observed number is NOT zero. E.g., the second last ICQC (Helsinki 2009) had lectures by Odile Eisenstein, Leticia Gonzáles, Emily A. Carter (one of the three signers of the current petition), Claudia Filippi and Nancy Makri. > > Five is not zero. > > Last time (ICQC Boulder 2012), there were Giulia Galli, Barbara Kirchner and Vlasta Bonacić-Koutecký. > > Three is not zero. > > > [I'm not touching the issue of what is the correct amount per gender.] > -- > --------------------------------------------------------------- > Mr. Susi Lehtola, PhD Research Associate > susi.lehtola*o*alumni.helsinki.fi Department of Applied Physics > http://www.helsinki.fi/~jzlehtol Aalto University > Finland > --------------------------------------------------------------- > Susi Lehtola, FT Tutkijatohtori > susi.lehtola*o*alumni.helsinki.fi Fysiikan laitos > http://www.helsinki.fi/~jzlehtol Aalto-yliopisto > --------------------------------------------------------------- From owner-chemistry@ccl.net Thu Feb 20 09:40:01 2014 From: "tamer sabry abd allah t_sabry2005(a)hotmail.com" To: CCL Subject: CCL: CASTEP-core hole effect Message-Id: <-49776-140220093654-12524-yrntrnPzbGvwmBwj34pxVA(a)server.ccl.net> X-Original-From: "tamer sabry abd allah" Date: Thu, 20 Feb 2014 09:36:53 -0500 Sent to CCL by: "tamer sabry abd allah" [t_sabry2005(0)hotmail.com] Dear CCL members Regarding crystal electronic propeties calculations using CASTEP, could someone explain how/when core hole be used? kindest Regards Tamer sabry t_sabry2005(_)hotmail.com From owner-chemistry@ccl.net Thu Feb 20 10:38:00 2014 From: "Soren Eustis seustis-$-bowdoin.edu" To: CCL Subject: CCL: Fall ACS Symposium Call for Papers: Theoretical and Computational Approaches to Environmental Chemistry Message-Id: <-49777-140220103454-6300-cQh0tjDwxnUX350HDx7A/w!A!server.ccl.net> X-Original-From: Soren Eustis Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_093092221880C24F8F0ABB6CC6A35D6D9DB3BCADEXCH2010MB2bowd_" Date: Thu, 20 Feb 2014 15:33:21 +0000 MIME-Version: 1.0 Sent to CCL by: Soren Eustis [seustis^^^bowdoin.edu] --_000_093092221880C24F8F0ABB6CC6A35D6D9DB3BCADEXCH2010MB2bowd_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable CCLers, I would like to bring your attention to a symposium I am organizing for the= Environmental Chemistry Division at the Fall 2014 American Chemical Societ= y meeting in San Francisco. The symposium is entitled "Theoretical and Com= putational Approaches to Environmental Chemistry". The session description= is copied beneath this message. I hope to engage a wide range of scientists performing research in such are= as as computational chemistry, environmental modeling, and data analysis. = Registration is open until March 10, 2014 (http://www.acs.org/content/acs/e= n/meetings/fall-2014.html). Interested researchers can apply online through the URL listed above, and/o= r feel free to contact me (seustis]_[bowdoin.edu)= with any questions. Thank you for your time. Best Wishes, Soren "Description The tools of environmental chemistry have undergone a radical transformatio= n within the past few decades. Advances in analytical methods and instrume= ntation have provided unprecedented insight into the myriad of natural and = anthropogenic chemicals present in environmental systems. In addition, advances in high performance computing hardware and mathematic= al and statistical techniques have provided powerful new tools that can be = utilized to solve problems in environmental chemistry. This symposium is intended to showcase how theoretical and computational te= chniques can be used to understand reaction mechanisms, fate, toxicity, and= many other key parameters of interest to environmental chemists. Participants from a wide range of chemical disciplines are encouraged to pa= rticipate as computational techniques are now employed across the chemical = sciences. The topics that would be covered in this session, but not limited to, are: = Systems modeling, quantum chemistry (photochemistry, reaction mechanisms, e= tc.), data analysis, biodegradation modeling, in-silico toxicity prediction= , ab initio physical property determination." -- Soren N. Eustis Assistant Professor Department of Chemistry Bowdoin College 6600 College Station Brunswick, ME 04011 262 Druckenmiller Hall 207.725.3524 (Office) 207.721.5201 (Lab) 207.725.3405 (Fax) http://www.bowdoin.edu/faculty/s/seustis/ --_000_093092221880C24F8F0ABB6CC6A35D6D9DB3BCADEXCH2010MB2bowd_ Content-Type: text/html; charset="us-ascii" Content-ID: <71D5F7BE4C84534FA9A3A2C894592140]_[bowdoin.edu> Content-Transfer-Encoding: quoted-printable
CCLers,

I would like to bring your attention to a s= ymposium I am organizing for the Environmental Chemistry Division at the Fa= ll 2014 American Chemical Society meeting in San Francisco.  The sympo= sium is entitled "Theoretical and Computational Approaches to Environmental Chemistry".  The session description= is copied beneath this message.

I hope to engage a wide range of scientists= performing research in such areas as computational chemistry, environmenta= l modeling, and data analysis.  Registration is open until March 10, 2= 014 (= http://www.acs.org/content/acs/en/meetings/fall-2014.html). 

Interested researchers can apply online thr= ough the URL listed above, and/or feel free to contact me (seustis]_[bowdoin.edu) with any questions.  T= hank you for your time.  

Best Wishes,

Soren

"Description

The tools of environmental chemistry h= ave undergone a radical transformation within the past few decades.  A= dvances in analytical methods and instrumentation have provided unprecedent= ed insight into the myriad of natural and anthropogenic chemicals present in environmental systems.  
In addition, advances = in high performance computing hardware and mathematical and statistical tec= hniques have provided powerful new tools that can be utilized to solve prob= lems in environmental chemistry.  
This symposium is inte= nded to showcase how theoretical and computational techniques can be used t= o understand reaction mechanisms, fate, toxicity, and many other key parame= ters of interest to environmental chemists.  
Participants from a wi= de range of chemical disciplines are encouraged to participate as computati= onal techniques are now employed across the chemical sciences.    = ; 

The topics that would be covered in th= is session, but not limited to, are: Systems modeling, quantum chemistry (p= hotochemistry, reaction mechanisms, etc.), data analysis, biodegradation mo= deling, in-silico toxicity prediction, ab initio physical property determination." 


--
Soren N. Eustis
Assistant Professor
Department of Chemistry
Bowdoin College
6600 College Station
Brunswick, ME 04011

262 Druckenmiller Hall
207.725.3524 (Office)
207.721.5201 (Lab)
207.725.3405 (Fax)

--_000_093092221880C24F8F0ABB6CC6A35D6D9DB3BCADEXCH2010MB2bowd_-- From owner-chemistry@ccl.net Thu Feb 20 11:24:00 2014 From: "Zork Zou zorkzou|,|gmail.com" To: CCL Subject: CCL:G: GAUSSIAN/GAMESS/MOLPRO/CRYSTAL: different energies - f function basis Message-Id: <-49778-140220100205-23896-ivxrZrvIj0IcXD8xJkGTaw/a\server.ccl.net> X-Original-From: Zork Zou Content-Type: multipart/alternative; boundary=001a11c2fccaf6889b04f2d7c8bb Date: Thu, 20 Feb 2014 09:01:50 -0600 MIME-Version: 1.0 Sent to CCL by: Zork Zou [zorkzou---gmail.com] --001a11c2fccaf6889b04f2d7c8bb Content-Type: text/plain; charset=ISO-8859-1 Dear Mike, The reason is that the initial occulation of MOLPRO and GAMESS is (a1)2 (t2)6 (a1)2, whereas in GAUSSIAN is (a1)2 (t2)6 (t2)2. The GAUSSIAN energy can be reproduced by using the following commands. MOLPRO: {hf;noenest;occ,1,2,1,1} GAMESS: $GUESS NORDER=1 IORDER(2)=6,3,4,5,2 $END To reproduce MOLPRO/GAMESS energy by GAUSSIAN, use #p HF/GEN symm=loose guess=alter iop(5/15=2) and insert 5 8 at the end of your input file. Best regards, Wenli On Wed, Feb 19, 2014 at 11:30 AM, Mike Towler mdt26-.-cam.ac.uk < owner-chemistry(_)ccl.net> wrote: > > Sent to CCL by: "Mike Towler" [mdt26*cam.ac.uk] > Hello, > > I'm one of the authors of the CASINO program - a widely-used quantum Monte > Carlo code: http://vallico.net/casinoqmc/ . The way QMC works, CASINO > reads a 'trial wave function' generated by an external code using e.g. a > Hartree-Fock or a DFT calculation, and then it proceeds to 'improve the > answer' (details irrelevant). I'm therefore responsible for maintaining > interfaces between CASINO and other people's software - a list of the > fifteen codes we supposedly support is here: > > http://vallico.net/casinoqmc/interfaces > > For the purposes of my present question, this list includes GAUSSIAN, > GAMESS, CRYSTAL, and MOLPRO. > > I've recently started a formal check of the way these interfaces handle > higher angular momentum Gaussian functions (by which I mean f and g along > with d for completeness). The complexity of the expressions and the > different conventions in use mean that this sort of thing is very easy to > screw up. > > Basic checks are simple enough, since (1) CASINO does a numerical check of > its own analytic derivatives (it needs the value of the orbitals, the > gradient, and the Laplacian at random points in configuration space), and > (2) CASINO is capable of running in pure Hartree-Fock mode, and thus > through Monte Carlo numerical integration it should be able to give the > same Hartree-Fock energy (within statistical error bars) as the code that > generated the trial wave function. > > To check the different angular momenta individually, I've created a set of > three input files for the methane molecule, with only d functions in the > basis, only f functions, and only g functions (let's call them 'd-ane', > 'f-ane', and 'g-ane'). > > However, before we even get to CASINO, and looking first at f-ane, we've > found that the four codes above give very different answers for the > Hartree-Fock energy. In fact GAUSSIAN and CRYSTAL give -11.3966 au, but > both GAMESS and MOLPRO give -11.2286 au. > > (For the record, CASINO agrees with GAUSSIAN and CRYSTAL for the HF energy > when fed with their trial wave functions. It's not been possible to check > with GAMESS and MOLPRO as their current interfaces to CASINO don't yet > support f functions.. though they will shortly.) > > Now I don't have the experience or any access to any of these codes apart > > from CRYSTAL (I got some kind colleagues to run the calculations for me), > so it's difficult for me to see why this difference exists, and my > colleagues aren't sure either. There was some suggestion that it might be > to do with the spherical/Cartesian basis set conversion? So I was > wondering, are there any GAMESS, GAUSSIAN, or MOLPRO gurus out there who > can shed any light on this problem? It seems strange that such well-known > codes would give such different answers for such a simple system. > > The input files for the four codes are here: > > http://www.tcm.phy.cam.ac.uk/~mdt26/g/crystal.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/gamess.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/gaussian.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro1.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro2.txt > > Any assistance will be gratefully appreciated. > > Thanks, > Mike Towler> > > --001a11c2fccaf6889b04f2d7c8bb Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Mike,

The reason is tha= t the initial occulation of MOLPRO and GAMESS is (a1)2 (t2)6 (a1)2, whereas= in GAUSSIAN
is (a1)2 (t2)6 (t2)2.

The G= AUSSIAN energy can be reproduced by using the following commands.
MOLPRO:
{hf;noenest;occ,1,2,1,1}

GA= MESS:
=A0$GUESS =A0NORDER=3D1 IORDER(2)=3D6,3,4,5,2 $END

To reproduce MOLPRO/GAMESS energy by GAUSSIAN, use
#p HF/GEN symm=3Dloose guess=3Dalter iop(5/15=3D2)
and insert

5 8
at the end of your i= nput file.

Best regards,
Wenli


On Wed, Feb= 19, 2014 at 11:30 AM, Mike Towler mdt26-.-cam= .ac.uk <owner-chemistry(_)ccl.net> wrote:

Sent to CCL by: "Mike =A0Towler" [mdt26*cam.ac.uk]
Hello,

I'm one of the authors of the CASINO program - a widely-used quantum Mo= nte
Carlo code: htt= p://vallico.net/casinoqmc/ . The way QMC works, CASINO
reads a 'trial wave function' generated by an external code using e= .g. a
Hartree-Fock or a DFT calculation, and then it proceeds to 'improve the=
answer' (details irrelevant). I'm therefore responsible for maintai= ning
interfaces between CASINO and other people's software - a list of the fifteen codes we supposedly support is here:

http:= //vallico.net/casinoqmc/interfaces

For the purposes of my present question, this list includes GAUSSIAN,
GAMESS, CRYSTAL, and MOLPRO.

I've recently started a formal check of the way these interfaces handle=
higher angular momentum Gaussian functions (by which I mean f and g along with d for completeness). The complexity of the expressions and the
different conventions in use mean that this sort of thing is very easy to screw up.

Basic checks are simple enough, since (1) CASINO does a numerical check of<= br> its own analytic derivatives (it needs the value of the orbitals, the
gradient, and the Laplacian at random points in configuration space), and (2) CASINO is capable of running in pure Hartree-Fock mode, and thus
through Monte Carlo numerical integration it should be able to give the
same Hartree-Fock energy (within statistical error bars) as the code that generated the trial wave function.

To check the different angular momenta individually, I've created a set= of
three input files for the methane molecule, with only d functions in the basis, only f functions, and only g functions (let's call them 'd-a= ne',
'f-ane', and 'g-ane').

However, before we even get to CASINO, and looking first at f-ane, we'v= e
found that the four codes above give very different answers for the
Hartree-Fock energy. In fact GAUSSIAN and CRYSTAL give -11.3966 au, but
both GAMESS and MOLPRO give -11.2286 au.

(For the record, CASINO agrees with GAUSSIAN and CRYSTAL for the HF energy<= br> when fed with their trial wave functions. It's not been possible to che= ck
with GAMESS and MOLPRO as their current interfaces to CASINO don't yet<= br> support f functions.. though they will shortly.)

Now I don't have the experience or any access to any of these codes apa= rt
> from CRYSTAL (I got some kind colleagues to run the calculations for m= e),
so it's difficult for me to see why this difference exists, and my
colleagues aren't sure either. There was some suggestion that it might = be
to do with the spherical/Cartesian basis set conversion? =A0So I was
wondering, are there any GAMESS, GAUSSIAN, or MOLPRO gurus out there who can shed any light on this problem? It seems strange that such well-known codes would give such different answers for such a simple system.

The input files for the four codes are here:

http://www.tcm.phy.cam.ac.uk/~mdt26/g/crystal.txt
http://www.tcm.phy.cam.ac.uk/~mdt26/g/gamess.txt
http://www.tcm.phy.cam.ac.uk/~mdt26/g/gaussian.txt
http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro1.txt
http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro2.txt

Any assistance will be gratefully appreciated.

Thanks,
Mike Towler



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY(_)ccl.n= et or use:
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST(_)ccl.net or use
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0 h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--001a11c2fccaf6889b04f2d7c8bb-- From owner-chemistry@ccl.net Thu Feb 20 13:54:01 2014 From: "James Prudhomme jprudhomme(-)healthtech.com" To: CCL Subject: CCL: Structure-Based Drug Design Message-Id: <-49779-140220131930-21498-YmmI2mdmh04vSPfK74ridw]_[server.ccl.net> X-Original-From: "James Prudhomme" Date: Thu, 20 Feb 2014 13:19:03 -0500 Sent to CCL by: "James Prudhomme" [jprudhomme{=}healthtech.com] Structure-Based Drug Design: Using Structure and Rational Design to Accelerate Discovery May 21-22, 2014 Westin Boston Waterfront, Boston, MA Experimental methods such as X-ray crystallography, NMR, and computational chemistry techniques have led to a better understanding and larger knowledge base of 3-dimensional structures and binding events, encouraging rapid development of structure-based drug design. This conference will showcase informative, high-quality case studies, innovative techniques, and strategies to move from computation to experiment, and finally, to drug. Top scientists from pharma and biotech will address how they are hitting epigenetic targets, provide updates on the newest wave of GPCRs and other membrane proteins, and discuss the latest in fragment-based drug design. Organized by: Cambridge Healthtech Institute Sponsored by: OpenEye, Schrodinger, International Society for Computational Biology (ISCB), and Bio-IT World. For more information and a link to the online registration form, go to http://www.healthtech.com/structure-based-drug-design Academia/government institutes interested in sharing their work via a research poster are encouraged to do so. *Poster Application deadline:* April 4, 2014 I am happy to answer any of your questions. Thank you. Regards, James Prudhomme Senior Marketing Manager Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 Tel: 781-972-5400 jprudhomme+/-healthtech.com From owner-chemistry@ccl.net Thu Feb 20 14:29:01 2014 From: "James Prudhomme jprudhomme[-]healthtech.com" To: CCL Subject: CCL: Structure-Based Drug Design: Using Structure and Rational Design to Accelerate Discovery Message-Id: <-49780-140220132116-21873-6hgIRLTauDmQzBOHDi/flQ]^[server.ccl.net> X-Original-From: "James Prudhomme" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0086_01CF2E3F.10385BA0" Date: Thu, 20 Feb 2014 13:24:20 -0500 MIME-Version: 1.0 Sent to CCL by: "James Prudhomme" [jprudhomme\a/healthtech.com] This is a multipart message in MIME format. ------=_NextPart_000_0086_01CF2E3F.10385BA0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Structure-Based Drug Design: Using Structure and Rational Design to Accelerate Discovery May 21-22, 2014 Westin Boston Waterfront, Boston, MA Experimental methods such as X-ray crystallography, NMR, and computational chemistry techniques have led to a better understanding and larger knowledge base of 3-dimensional structures and binding events, encouraging rapid development of structure-based drug design. This conference will showcase informative, high-quality case studies, innovative techniques, and strategies to move > from computation to experiment, and finally, to drug. Top scientists from pharma and biotech will address how they are hitting epigenetic targets, provide updates on the newest wave of GPCRs and other membrane proteins, and discuss the latest in fragment-based drug design. Organized by: Cambridge Healthtech Institute Sponsored by: OpenEye, Schrodinger, International Society for Computational Biology (ISCB), and Bio-IT World. For more information and a link to the online registration form, go to http://www.healthtech.com/structure-based-drug-design Academia/government institutes interested in sharing their work via a research poster are encouraged to do so. *Poster Application Deadline:* April 4, 2014 I am happy to answer any of your questions. Thank you. Regards, James Prudhomme Senior Marketing Manager Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 Tel: 781-972-5400 jprudhomme^^healthtech.com ------=_NextPart_000_0086_01CF2E3F.10385BA0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Structure-Based Drug Design: Using = Structure and Rational Design to Accelerate Discovery
May 21-22, 2014
Westin Boston Waterfront, Boston, MA

Experimental methods such as X-ray crystallography, NMR, and = computational chemistry techniques have
led to a better understanding and larger knowledge base of 3-dimensional structures and binding events,
encouraging rapid development of structure-based drug design. This = conference will showcase informative,
high-quality case studies, innovative techniques, and strategies to move = > from computation to experiment,
and finally, to drug. Top scientists from pharma and biotech will = address how they are hitting epigenetic
targets, provide updates on the newest wave of GPCRs and other membrane proteins, and discuss the
latest in fragment-based drug design.

Organized by: Cambridge Healthtech = Institute

Sponsored by: OpenEye, Schrodinger, International Society for = Computational Biology (ISCB), and Bio-IT World.

For more information and a link to the online registration form, go to http://www= .healthtech.com/structure-based-drug-design

 

Academia/gove= rnment institutes interested in sharing their work via a research poster are encouraged to do so.

 

*Poster Application Deadline:* April 4, 2014


I am happy to answer any of your questions.  Thank you.

Regards,

James Prudhomme
Senior Marketing Manager
Cambridge Healthtech Institute
250 First Avenue, Suite 300
Needham, MA 02494
Tel: 781-972-5400
jprudhomme^^healthtech.com =

------=_NextPart_000_0086_01CF2E3F.10385BA0-- From owner-chemistry@ccl.net Thu Feb 20 20:47:00 2014 From: "Phil Hasnip phil.hasnip^^^york.ac.uk" To: CCL Subject: CCL: CASTEP-core hole effect Message-Id: <-49781-140220195415-19176-HWxMflBsrwh1Cv5LTc2S6A~!~server.ccl.net> X-Original-From: Phil Hasnip Content-Type: multipart/alternative; boundary=001a11c20c5434580604f2e00fa4 Date: Fri, 21 Feb 2014 00:54:08 +0000 MIME-Version: 1.0 Sent to CCL by: Phil Hasnip [phil.hasnip-#-york.ac.uk] --001a11c20c5434580604f2e00fa4 Content-Type: text/plain; charset=ISO-8859-1 Dear Tamer, The core-hole is not usually used when computing general electronic structure properties, but it is used when computing electron-energy loss spectra (EELS) -- also known as electron energy-loss near-edge spectra (ELNES) and X-ray absorption near-edge spectra (XANES). In these experiments a core electron (i.e. one that is usually considered to be "frozen" in the pseudopotential) is excited from its low-energy state (usually by an incident high-energy electron or X-ray) up to a conduction state, leaving a "hole" in the core states, which is why it's called the core-hole. In order to simulate this in a pseudopotential code like CASTEP, you generate a pseudopotential for one of the atoms which has one of the core electrons missing (usually a 1s electron for the so-called K-edge spectra). In CASTEP you can do this relatively simply with the on-the-fly pseudopotential generator, see for example the tutorial for using OptaDOS with CASTEP at http://www.castep.org/Tutorials/CoreLossEELS. All the best, Phil Hasnip On 20 February 2014 14:36, tamer sabry abd allah t_sabry2005(a)hotmail.com < owner-chemistry%%ccl.net> wrote: > > Sent to CCL by: "tamer sabry abd allah" [t_sabry2005(0)hotmail.com] > Dear CCL members > Regarding crystal electronic propeties calculations using CASTEP, could > someone explain how/when core hole be used? > kindest Regards > Tamer sabry > t_sabry2005|a|hotmail.com> > > -- ----------------------------------------------------------------------------- Dr Phil Hasnip Email: phil.hasnip%%york.ac.uk Dept of Physics University of York Tel: +44 (0)1904 324624 York YO10 5DD --001a11c20c5434580604f2e00fa4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Tamer,

The core-hole is not us= ually used when computing general electronic structure properties, but it i= s used when computing electron-energy loss spectra (EELS) -- also known as = electron energy-loss near-edge spectra (ELNES) and X-ray absorption near-ed= ge spectra (XANES). In these experiments a core electron (i.e. one that is = usually considered to be "frozen" in the pseudopotential) is exci= ted from its low-energy state (usually by an incident high-energy electron = or X-ray) up to a conduction state, leaving a "hole" in the core = states, which is why it's called the core-hole.

In order to simulate this in a pseudopotential code like CASTEP, you ge= nerate a pseudopotential for one of the atoms which has one of the core ele= ctrons missing (usually a 1s electron for the so-called K-edge spectra). In= CASTEP you can do this relatively simply with the on-the-fly pseudopotenti= al generator, see for example the tutorial for using OptaDOS with CASTEP a= t http://www.caste= p.org/Tutorials/CoreLossEELS.

All the best,

Phil Hasnip


On 20 February 2014 14:36, tamer sab= ry abd allah t_sabry2005(a)hotmail.com <= span dir=3D"ltr"><owner-chemistry%%ccl.net> wrote:

Sent to CCL by: "tamer sabry abd allah" [t_sabry2005(0)hotmail.com]
Dear CCL members
Regarding crystal electronic propeties calculations using CASTEP, could som= eone explain how/when core hole be used?
kindest Regards
Tamer sabry
t_sabry2005|a|hotmail.com<= /a>



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY%%ccl.n= et or use:
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST%%ccl.net or use
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0 h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
-----------------------= ------------------------------------------------------
Dr Phil Hasnip = =A0 =A0 =A0 =A0 =A0 =A0Email: phil.hasnip%%york.ac.uk
Dept of Physics
University of York =A0 =A0 =A0 =A0Tel: =A0+44 (0)1904 32= 4624
York YO10 5DD
--001a11c20c5434580604f2e00fa4-- From owner-chemistry@ccl.net Thu Feb 20 21:22:00 2014 From: "Miquel Sola miquel.sola|a|udg.edu" To: CCL Subject: CCL: XI Girona Seminar 2014 Registration-Abstract Submission Message-Id: <-49782-140220171029-2213-MqEBLsYsfZ9HhLhvA63Avw(-)server.ccl.net> X-Original-From: Miquel Sola Content-Type: multipart/alternative; boundary="------------080708080201000708040103" Date: Thu, 20 Feb 2014 23:10:25 +0100 MIME-Version: 1.0 Sent to CCL by: Miquel Sola [miquel.sola-#-udg.edu] This is a multi-part message in MIME format. --------------080708080201000708040103 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear colleague, The XI Girona Seminar on Carbon, Metal, and Carbon-Metal Clusters: From Theory to Applications is already open for registration. You can register in the following link: http://xigironaseminar2014.wordpress.com/registration/ The standard registration fee is 550 EUR, whereas the reduced registration fee for PhD students is 300 EUR. The registration fee includes coffee-breaks, lunches, social events and the conference dinner. The deadline for registration is May 1 2014. Details about the payment can be found in the webpage. List of invited speakers is available at: http://xigironaseminar2014.wordpress.com/lectures/ Researchers have the opportunity to present their research as a short communication. As the number of short communications is reduced, the scientific committee will select them from the abstracts received, the rest will be accepted as a poster. The deadline for abstract submission is April 1 2014, and the accepted ones as communications will be announced on April 7 2014 at the conference website (please check: http://xigironaseminar2014.wordpress.com/abstracts/). The attendees of the XI Girona Seminar are also encouraged to submit an article to the invited special issue in the /Theoretical Chemistry Accounts/ journal. For more information regarding the TCA contribution, please check http://xigironaseminar2014.wordpress.com/issue-tca/. For further information, do not hesitate to contact us via gisem2014::gmail.com . We are looking forward to seeing you all in Girona next summer! Best regards, **XI Girona Seminar Organizing Committee Miquel Solà (Chairman) Sílvia Osuna (Vice-Chairman) Jordi Poater (Secretary) Organized by the Institute of Computational Chemistry and Catalysis of the University of Girona (http:/iqcc.udg.edu) --------------080708080201000708040103 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Dear colleague,

The XI Girona Seminar on Carbon, Metal, and Carbon-Metal Clusters: From Theory to Applications is already open for registration. You can register in the following link: http://xigironaseminar2014.wordpress.com/registration/

The standard registration fee is 550 EUR, whereas the reduced registration fee for PhD students is 300 EUR. The registration fee includes coffee-breaks, lunches, social events and the conference dinner. The deadline for registration is May 1 2014. Details about the payment can be found in the webpage.

List of invited speakers is available at: http://xigironaseminar2014.wordpress.com/lectures/

Researchers have the opportunity to present their research as a short communication. As the number of short communications is reduced, the scientific committee will select them from the abstracts received, the rest will be accepted as a poster. The deadline for abstract submission is April 1 2014, and the accepted ones as communications will be announced on April 7 2014 at the conference website (please check: http://xigironaseminar2014.wordpress.com/abstracts/).

The attendees of the XI Girona Seminar are also encouraged to submit an article to the invited special issue in the Theoretical Chemistry Accounts journal. For more information regarding the TCA contribution, please check http://xigironaseminar2014.wordpress.com/issue-tca/.

For further information, do not hesitate to contact us via gisem2014::gmail.com.

We are looking forward to seeing you all in Girona next summer!

Best regards,

XI Girona Seminar Organizing Committee 
Miquel Solà (Chairman)
Sílvia Osuna (Vice-Chairman)
Jordi Poater (Secretary)

Organized by the Institute of Computational Chemistry and Catalysis of the University of Girona (http:/iqcc.udg.edu)

--------------080708080201000708040103-- From owner-chemistry@ccl.net Thu Feb 20 21:57:00 2014 From: "Violeta Isabel Perez Nueno pereznueno : harmonicpharma.com" To: CCL Subject: CCL: "Drug discovery: Computer models can predict side effect targets" at ICCMSE 2014 Meeting. Deadline abstracts submission: February 28, 2014 Message-Id: <-49783-140220172839-5247-mFGd8PwUkLTO+5mrybmAcg\a/server.ccl.net> X-Original-From: Violeta Isabel Perez Nueno Content-Type: multipart/alternative; boundary="Apple-Mail=_40735A40-8AAC-4435-BAE3-39017DA300DC" Date: Thu, 20 Feb 2014 23:28:28 +0100 Mime-Version: 1.0 (Apple Message framework v1280) Sent to CCL by: Violeta Isabel Perez Nueno [pereznueno|-|harmonicpharma.com] --Apple-Mail=_40735A40-8AAC-4435-BAE3-39017DA300DC Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 "Drug discovery: Computer models can predict side effect targets" at = ICCMSE 2014 Meeting (http://www.iccmse.org/abstract.htm) 04-07/04/2014 Athens, Greece, Metropolitan Hotel:http://www.chandris.gr/athens/, URL = address: http://www.iccmse.org/ "Nowadays, the polypharmacology of promiscuous binders is recognized as = an important aspect in drug design. Pharmaceutical companies are = discovering increasing numbers of promiscuous targets and promiscuous = ligands. Both of these phenomena are clearly of great importance when = considering drug side-effects. The in silico prediction of unwanted side = effects caused by the promiscuous behavior of drugs and their targets is = highly relevant to the pharmaceutical industry. Considerable effort is = now being put into the computational and experimental screening of = several suspected off-target proteins in the hope that side effects = might be identified early, before the cost associated with developing a = drug candidate rises steeply. On the other hand, promiscuity is not = always unwelcome and it can even be exploited for drug development. This = symposium will cover network pharmacology/systems biology approaches = which provide understanding of diseases and drug effects, and = polypharmacology approaches which allow repurposing of existing drugs = with known targets." The goal of this symposium is to widely cover experts on drug discovery = to help develop faster, more robust, and highly predictive drug = promiscuity approaches with the idea of advancing drug design in a wider = =93systems-level=94 context.=20 Abstracts for posters and talks may be submitted via e-mail to = pereznueno=harmonicpharma.com. DEADLINE February 28, 2014.=20 IMPORTANT DATES: http://www.iccmse.org/schedule.htm, = http://www.iccmse.org/callfor.htm For more information and a link to the online registration form, go to = http://www.iccmse.org/ The Proceedings of ICCMSE 2014 will be published in the famous AIP = (American Institute of Physics) Conference Proceedings, which will be = abstracted/indexed in: ISI Proceedings, Zentrablatt fur Mathematik, = MathSciNet, Scopus, INSPEC, Scirus, Google Scholar etc.. More = information can be found at:http://www.iccmse.org/proceeding.htm . = Selected Proceedings of ICCMSE 2014 will be published in appropriate = journals. I am happy to answer any of your questions. Thank you. Best regards, Violeta Isabel Perez Nueno -- Violeta I. Perez-Nueno, Ph.D. Senior Scientist Harmonic Pharma Headquarter 615 rue du Jardin Botanique 54600 Villers l=E8s Nancy - France Cell +33(0) 638 878 547 ; Tel +33(0) 354 958 604 =96 Fax +33(0) 383 275 = 652 pereznueno=harmonicpharma.com =20 W: http://www.loria.fr/~pereznue/ Harmonic Pharma Asia Office MT Bldg 9F, 3-19 Hayabusacho, Chiyoda-ku Tokyo 102-0092 - Japan Tel +81(0)3 3288 9098 =96 Fax +81(0)3 3288 9099 www.harmonicpharma.com --Apple-Mail=_40735A40-8AAC-4435-BAE3-39017DA300DC Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252
http://www.iccmse.org/abstract= .htm)
 04-07/04/2014
http://www.iccmse.org/

"Nowadays, the polypharmacology = of promiscuous binders is recognized as an important aspect in drug = design. Pharmaceutical companies are discovering increasing numbers of = promiscuous targets and promiscuous ligands. Both of these phenomena are = clearly of great importance when considering drug side-effects. The in = silico prediction of unwanted side effects caused by the promiscuous = behavior of drugs and their targets is highly relevant to the = pharmaceutical industry. Considerable effort is now being put into the = computational and experimental screening of several suspected off-target = proteins in the hope that side effects might be identified early, before = the cost associated with developing a drug candidate rises steeply. On = the other hand, promiscuity is not always unwelcome and it can even be = exploited for drug development. This symposium will cover network = pharmacology/systems biology approaches which provide understanding of = diseases and drug effects, and polypharmacology approaches which allow = repurposing of existing drugs with known targets."
Abstracts for posters and talks may be = submitted via e-mail to pereznueno=harmonicpharma.co= m. DEADLINE February 28, 2014. 
http://www.iccmse.org/schedule= .htm,  http://www.iccmse.org/callfor.h= tm

http://www.iccmse.org/
The Proceedings of ICCMSE 2014 will be = published in the famous AIP (American Institute of Physics) Conference = Proceedings, which will be abstracted/indexed in: ISI Proceedings, = Zentrablatt fur Mathematik, MathSciNet, Scopus, INSPEC, Scirus, Google = Scholar etc.. More information can be found = at:http://www.iccmse.org/proceeding.htm .  Selected Proceedings of = ICCMSE 2014 will be published in appropriate journals.

I am happy to answer any of your = questions.  Thank you.


Violeta I. Perez-Nueno, Ph.D.Senior ScientistHarmonic Pharma Headquarter615 rue du Jardin Botanique54600 Villers l=E8s Nancy - FranceCell +33(0) 638 878 547 ;  Tel +33(0) 354 = 958 604 =96 Fax +33(0) 383 275 652
pereznueno=harmonicpharma.co= m  
http://www.loria.fr/~pereznue/=
Harmonic Pharma Asia = Office
MT Bldg 9F, 3-19 Hayabusacho, = Chiyoda-ku
Tokyo 102-0092 - Japan
Tel = +81(0)3 3288 9098 =96 Fax +81(0)3 3288 9099www.harmonicpharma.com<= /div>

= --Apple-Mail=_40735A40-8AAC-4435-BAE3-39017DA300DC-- From owner-chemistry@ccl.net Thu Feb 20 22:32:00 2014 From: "Violeta Isabel Perez Nueno pereznueno|-|harmonicpharma.com" To: CCL Subject: CCL: "Drug discovery: Computer models can predict side effect targets" at ICCMSE 2014 Meeting. Deadline abstracts submission: February 28, 2014 Message-Id: <-49784-140220173550-6495-pxGZmF0KtZr43cKDWa0zYQ===server.ccl.net> X-Original-From: Violeta Isabel Perez Nueno Content-Type: multipart/alternative; boundary="Apple-Mail=_BA060083-1812-4077-AE4C-DB477BD6F1F8" Date: Thu, 20 Feb 2014 23:35:42 +0100 Mime-Version: 1.0 (Apple Message framework v1280) Sent to CCL by: Violeta Isabel Perez Nueno [pereznueno]~[harmonicpharma.com] --Apple-Mail=_BA060083-1812-4077-AE4C-DB477BD6F1F8 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 "Drug discovery: Computer models can predict side effect targets" at = ICCMSE 2014 Meeting (http://www.iccmse.org/abstract.htm) 04-07/04/2014 Athens, Greece, Metropolitan Hotel:http://www.chandris.gr/athens/, URL = address: http://www.iccmse.org/ "Nowadays, the polypharmacology of promiscuous binders is recognized as = an important aspect in drug design. Pharmaceutical companies are = discovering increasing numbers of promiscuous targets and promiscuous = ligands. Both of these phenomena are clearly of great importance when = considering drug side-effects. The in silico prediction of unwanted side = effects caused by the promiscuous behavior of drugs and their targets is = highly relevant to the pharmaceutical industry. Considerable effort is = now being put into the computational and experimental screening of = several suspected off-target proteins in the hope that side effects = might be identified early, before the cost associated with developing a = drug candidate rises steeply. On the other hand, promiscuity is not = always unwelcome and it can even be exploited for drug development. This = symposium will cover network pharmacology/systems biology approaches = which provide understanding of diseases and drug effects, and = polypharmacology approaches which allow repurposing of existing drugs = with known targets." The goal of this symposium is to widely cover experts on drug discovery = to help develop faster, more robust, and highly predictive drug = promiscuity approaches with the idea of advancing drug design in a wider = =93systems-level=94 context.=20 Abstracts for posters and talks may be submitted via e-mail to = pereznueno,harmonicpharma.com. DEADLINE February 28, 2014.=20 IMPORTANT DATES: http://www.iccmse.org/schedule.htm, = http://www.iccmse.org/callfor.htm For more information and a link to the online registration form, go to = http://www.iccmse.org/ The Proceedings of ICCMSE 2014 will be published in the famous AIP = (American Institute of Physics) Conference Proceedings, which will be = abstracted/indexed in: ISI Proceedings, Zentrablatt fur Mathematik, = MathSciNet, Scopus, INSPEC, Scirus, Google Scholar etc.. More = information can be found at:http://www.iccmse.org/proceeding.htm . = Selected Proceedings of ICCMSE 2014 will be published in appropriate = journals. I am happy to answer any of your questions. Thank you. Best regards, Violeta Isabel Perez Nueno -- Violeta I. Perez-Nueno, Ph.D. Senior Scientist Harmonic Pharma Headquarter 615 rue du Jardin Botanique 54600 Villers l=E8s Nancy - France Cell +33(0) 638 878 547 ; Tel +33(0) 354 958 604 =96 Fax +33(0) 383 275 = 652 pereznueno,harmonicpharma.com =20 W: http://www.loria.fr/~pereznue/ Harmonic Pharma Asia Office MT Bldg 9F, 3-19 Hayabusacho, Chiyoda-ku Tokyo 102-0092 - Japan Tel +81(0)3 3288 9098 =96 Fax +81(0)3 3288 9099 www.harmonicpharma.com --Apple-Mail=_BA060083-1812-4077-AE4C-DB477BD6F1F8 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252
http://www.iccmse.org/abstract= .htm)
 04-07/04/2014
http://www.iccmse.org/

"Nowadays, the polypharmacology = of promiscuous binders is recognized as an important aspect in drug = design. Pharmaceutical companies are discovering increasing numbers of = promiscuous targets and promiscuous ligands. Both of these phenomena are = clearly of great importance when considering drug side-effects. The in = silico prediction of unwanted side effects caused by the promiscuous = behavior of drugs and their targets is highly relevant to the = pharmaceutical industry. Considerable effort is now being put into the = computational and experimental screening of several suspected off-target = proteins in the hope that side effects might be identified early, before = the cost associated with developing a drug candidate rises steeply. On = the other hand, promiscuity is not always unwelcome and it can even be = exploited for drug development. This symposium will cover network = pharmacology/systems biology approaches which provide understanding of = diseases and drug effects, and polypharmacology approaches which allow = repurposing of existing drugs with known targets."
Abstracts for posters and talks may be = submitted via e-mail to pereznueno,harmonicpharma.co= m. DEADLINE February 28, 2014. 
http://www.iccmse.org/schedule= .htm,  http://www.iccmse.org/callfor.h= tm

http://www.iccmse.org/
The Proceedings of ICCMSE 2014 will be = published in the famous AIP (American Institute of Physics) Conference = Proceedings, which will be abstracted/indexed in: ISI Proceedings, = Zentrablatt fur Mathematik, MathSciNet, Scopus, INSPEC, Scirus, Google = Scholar etc.. More information can be found = at:http://www.iccmse.org/proceeding.htm .  Selected Proceedings of = ICCMSE 2014 will be published in appropriate journals.

I am happy to answer any of your = questions.  Thank you.



--
Violeta I. Perez-Nueno, = Ph.D.
Senior Scientist
Harmonic Pharma = Headquarter
615 rue du Jardin Botanique
54600 = Villers l=E8s Nancy - France
Cell +33(0) 638 878 547 ;  Tel = +33(0) 354 958 604 =96 Fax +33(0) 383 275 652

Harmonic Pharma Asia Office
MT = Bldg 9F, 3-19 Hayabusacho, Chiyoda-ku
Tokyo 102-0092 - = Japan
Tel +81(0)3 3288 9098 =96 Fax +81(0)3 3288 = 9099
www.harmonicpharma.com<= /div>

= --Apple-Mail=_BA060083-1812-4077-AE4C-DB477BD6F1F8--