From owner-chemistry@ccl.net Wed Feb 4 04:55:01 2015 From: "Marc Raupach raupach**students.uni-marburg.de" To: CCL Subject: CCL: Long range and short range functional Message-Id: <-50990-150204035117-18438-Gf932Oxxv/lQaTgr9uK80A*server.ccl.net> X-Original-From: Marc Raupach Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=iso-8859-15; format=flowed Date: Wed, 04 Feb 2015 09:51:00 +0100 MIME-Version: 1.0 Sent to CCL by: Marc Raupach [raupach()students.uni-marburg.de] To understand the motivation behind different levels of approximation of DFT I suggest you look into reviews which discuss that issue. For example: Fifty years of density-functional theory in chemical physics by Axel Becke, The Journal of Chemical Physics 140, 18A301 (2014); doi: 10.1063/1.4869598 Long-range corrected density functional approximation: You split the electron-electron interaction 1/r_(12) into a short and a long range part, where the short range part is "approximated" and the long range part is treated as exactly as possible. The definition of short and long range part is of course the drawback of this scheme. Greetings, Marc PS: for example short range functionals can be GGAs, meta-GGAs and hybrids. Am 03.02.2015 um 12:05 schrieb Raghav V raghav011986*gmail.com: > Sent to CCL by: "Raghav V" [raghav011986,,gmail.com] > Can someone please tell me what a long range corrected and short range functional means.> > From owner-chemistry@ccl.net Wed Feb 4 05:57:01 2015 From: "Varun Kundi Kundi chemvarun*gmail.com" To: CCL Subject: CCL: Excited State Calculations Message-Id: <-50991-150204055556-19300-iISZevllvk+yX9Trnayj4w*|*server.ccl.net> X-Original-From: "Varun Kundi Kundi" Date: Wed, 4 Feb 2015 05:55:54 -0500 Sent to CCL by: "Varun Kundi Kundi" [chemvarun^-^gmail.com] Hello Everybody, How to evaluate the total energy of the first excited state in the ground state geometry ES1(QS0) and the total energy of the first excited state in the excited state geometry ES1(QS1) using G09. From owner-chemistry@ccl.net Wed Feb 4 09:49:01 2015 From: "Zoe Cournia zcournia^_^bioacademy.gr" To: CCL Subject: CCL: EMBO Long-Term Fellowship Message-Id: <-50993-150204041530-24378-2Dd60tiueh6OGtTv/TBOtA_+_server.ccl.net> X-Original-From: "Zoe Cournia" Date: Wed, 4 Feb 2015 04:15:29 -0500 Sent to CCL by: "Zoe Cournia" [zcournia%x%bioacademy.gr] Applications are invited for an EMBO Long-Term Fellowship to join the lab of Zoe Cournia at the Biomedical Research Foundation of the Academy of Athens in Greece. We have a well-established program and looking for motivated post-docs from the EU. Please contact Zoe Cournia at zcournia _ bioacademy.gr if you are interested in applying. The eligibility criteria are as follows: -Applicants who already hold a PhD degree at the time of application are eligible to apply only if they passed their PhD exam in the two years prior to the respective application deadline -Applicants must have at least one first author publication accepted in press or published in an international peer reviewed journal at the time of application. -All applications must involve movement between countries. The receiving institute or the applicant's nationality must be from one of the EMBC Member States. -Applications to go to the country in which the PhD was obtained will not be considered. From owner-chemistry@ccl.net Wed Feb 4 10:24:00 2015 From: "David Soriano d.soriano++acellera.com" To: CCL Subject: CCL: New cloud computing service for running molecular dynamics simulations Message-Id: <-50994-150204092927-21541-o72E0km8Lt61bOKO0n4Prg-#-server.ccl.net> X-Original-From: "David Soriano" Date: Wed, 4 Feb 2015 09:29:25 -0500 Sent to CCL by: "David Soriano" [d.soriano**acellera.com] Dear all, I am pleased to announce the release of our latest edition of AceCloud. Acecloud simplifies the entry of MD to cloud computing, and allows running Gromacs and ACEMD jobs of any scale using Amazon Web Service (AWS). The AceCloud interface abstracts all interaction with the supporting cloud computing infrastructure, and emulates the experience of running simulations locally on ones own machine. For more info visit: http://www.acellera.com/products/acecloud-molecular-dynamics-cloud- computing/ and http://www.acellera.com/cloud-molecular-dynamics-simulation-acecloud/ We will be in Baltimore for the Biophysical meeting, where we will have a paper for distribution regarding this topic. Feel free to contact us at info**acellera.com for more info or swing by our poster LB84 on the 10th in Hall C. Best, The Acellera Team. info**acellera.com From owner-chemistry@ccl.net Wed Feb 4 10:59:00 2015 From: "David Soriano d.soriano/./acellera.com" To: CCL Subject: CCL: New cloud computing service for running molecular dynamics simulations Message-Id: <-50995-150204092927-21541-D0CHp55iRhu+KC01Y8W4Kg~!~server.ccl.net> X-Original-From: "David Soriano" Date: Wed, 4 Feb 2015 09:29:25 -0500 Sent to CCL by: "David Soriano" [d.soriano###acellera.com] Dear all, I am pleased to announce the release of our latest edition of AceCloud. Acecloud simplifies the entry of MD to cloud computing, and allows running Gromacs and ACEMD jobs of any scale using Amazon Web Service (AWS). The AceCloud interface abstracts all interaction with the supporting cloud computing infrastructure, and emulates the experience of running simulations locally on ones own machine. For more info visit: http://www.acellera.com/products/acecloud-molecular-dynamics-cloud- computing/ and http://www.acellera.com/cloud-molecular-dynamics-simulation-acecloud/ We will be in Baltimore for the Biophysical meeting, where we will have a paper for distribution regarding this topic. Feel free to contact us at info*acellera.com for more info or swing by our poster LB84 on the 10th in Hall C. Best, The Acellera Team. info*acellera.com From owner-chemistry@ccl.net Wed Feb 4 11:34:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor*|*fluor.quimica.uniovi.es" To: CCL Subject: CCL: Excited State Calculations Message-Id: <-50996-150204110610-13643-chrlNqinmlhFeBWu5IOtQA|,|server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Wed, 04 Feb 2015 17:01:58 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor]*[fluor.quimica.uniovi.es] On Wed, Feb 04, 2015 at 05:55:54AM -0500, Varun Kundi Kundi chemvarun*gmail.com wrote: > > Sent to CCL by: "Varun Kundi Kundi" [chemvarun^-^gmail.com] > Hello Everybody, > > How to evaluate the total energy of the first excited state in the ground > state geometry ES1(QS0) and the total energy of the first excited state in > the excited state geometry ES1(QS1) using G09. Varun, I don't know if there is a specific route for doing that but you can always do a calculation at a fixed geometry. Do that for any purpose you have. Regards, Dr. Víctor Luaña -- . . "La suma de la mediocridad y de la creatividad es / `' \ constante: a más de la una menos de la otra" /(o)(o)\ (Jorge Wasenberg, 2015) /`. \/ .'\ "mediocrity+creativity=constant" / '`'` \ (First Principle of thermodynamics,Universal version) | \'`'`/ | "Lo mediocre es peor que lo bueno, pero también es peor | |'`'`| | que lo malo, porque la mediocridad no es un grado, es una \/`'`'`'\/ actitud" ===(((==)))==================================+========================= ! Dr.Víctor Luaña ! Mediocre is worse than ! Departamento de Química Física y Analítica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor%%fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Wed Feb 4 12:09:01 2015 From: "Mehboob Alam mehboob.cu{}gmail.com" To: CCL Subject: CCL: Help needed for CASSCF computation either in g09 or in NWChem Message-Id: <-50997-150204095458-6102-1TX1ljP7QbCSnUe4f9MR0w##server.ccl.net> X-Original-From: Mehboob Alam Content-Type: multipart/alternative; boundary=001a11342f08a2490f050e445e36 Date: Wed, 4 Feb 2015 15:54:51 +0100 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu^^^gmail.com] --001a11342f08a2490f050e445e36 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Kaushik, One way to choose the active space is to look into the occupation number of the natural orbitals. I have done some MCSCF calculation but using the DALTON program package only. What I do is that I run a single point MP2 calculation using DALTON and analyse the natural orbital occupation which clearly tells which orbital is active and which is not. However for big molecules, it will be much time consuming. Regards, Mehboob Dr. Md. Mehboob Alam Post-Doctoral Researcher Institut de Chimie de Strasbourg Laboratoire de Chimie Quantique Universit=E9 de Strasbourg PostDoc Supervisor - Dr. Emmanuel Fromager On Wed, Feb 4, 2015 at 2:56 PM, Kaushik Hatua kaushikhatua|*|yahoo.in < owner-chemistry###ccl.net> wrote: > For CASSCF you can see the example in g09 website first. Since you > confirmed the intermediate as biradical then a minimum active space 2,2 i= s > needed. Actually it's very difficult to say. Active space selection is no= t > straightforward. Where is the two unpaired electron, which orbital they > reside all this are necessary. One black box technique can be adapted whe= re > all valence electrons are included in the active space. If the system is > big then it would be time consuming. > > Sent from Nokia Lumia > > -----Original Message----- > > From: "Rana, Anup rana[a]chemie.uni-siegen.de" ccl.net> > Sent: 03-02-2015 06:05 AM > To: "Hatua, Kaushik " > Subject: CCL: Help needed for CASSCF computation either in g09 or in NWCh= em > > > Sent to CCL by: "Rana, Anup" [rana*|*chemie.uni-siegen.de] > Hi all, > > Recently I performed one reaction and when I did DFT computation, I found > that the reaction is following a stepwise path involving biradical > intermediate. So far I know from literature that CASSCF can treat all tho= se > multireference problems very well. I have never done CASSCF computation a= nd > that is why I am worried about that. It would be really nice if someone > suggest me, step by step, how to do this computation either in g09 or in > NWChem. I am not a theoretician and that is why a clear technical aspect > would be really great for me. > > Thank you very much in advance. > > With best regards, > Anup Rana > > > > -=3D This is automatically added to each message by the mailing script = =3D---_1BFEA483-BEDE-4B22-9F0D-828A16B0EF11_ > Content-Transfer-Encoding: quoted-printable > Content-Type: text/html; charset"utf-8" > > charset=3Dutf-8">
Calibri,sans-serif; font-size: 11pt;">For CASSCF you can see the example = in > g09 website first. Since you confirmed the intermediate as biradical then= a > minimum active space 2,2 is needed. Actually it's very difficult to say. > Active space selection is not straightforward. Where is the two unpaired > electron, which orbital they reside all this are necessary. One black box > technique can be adapted where all valence electrons are included in the > active space. If the system is big then it would be time > consuming.

Sent from Nokia Lumia
dir=3D"ltr">
11pt; font-weight: bold;">From: Calibri,sans-serif; font-size: 11pt;"> ccl.net">Rana, Anup rana[a]chemie.uni-siegen.de
style=3D"font-family: Calibri,sans-serif; font-size: 11pt; font-weight: > bold;">Sent: font-size: 11pt;">03-02-2015 06:05 AM
style=3D"font-family: Calibri,sans-serif; font-size: 11pt; font-weight: > bold;">To: 11pt;">Hatua, Kaushik >
11pt; font-weight: bold;">Subject: Calibri,sans-serif; font-size: 11pt;">CCL: Help needed for CASSCF > computation either in g09 or in NWChem


Sent to CC= L > by: "Rana, Anup" [rana*|*chemie.uni-siegen.de]
Hi all,

Recently > I performed one reaction and when I did DFT computation, I found that the > reaction is following a stepwise path involving biradical intermediate. S= o > far I know from literature that CASSCF can treat all those multireference > problems very well. I have never done CASSCF computation and that is why = I > am worried about that. It would be really nice if someone suggest me, ste= p > by step, how to do this computation either in g09 or in NWChem. I am not = a > theoretician and that is why a clear technical aspect would be really gre= at > for me.

Thank you very much in advance.

With best > regards,
Anup Rana



-=3D This is automatically added to = each > message by the mailing script =3D-
look up the X-Original-From: > line in the mail header.

E-mail to subscribers: CHEMISTRY+/-ccl.ne= t > or use:
     

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Search > Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

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--001a11342f08a2490f050e445e36 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Kaushik,

One way to choose the activ= e space is to look into the occupation number of the natural orbitals. I ha= ve done some MCSCF calculation but using the DALTON program package only. W= hat I do is that I run a single point MP2 calculation using DALTON and anal= yse the natural orbital occupation which clearly tells which orbital is act= ive and which is not. However for big molecules, it will be much time consu= ming.

Regards,
Mehboob

Dr. Md. Mehboob Alam
Po= st-Doctoral Researcher
Institut de Chimie de Strasbourg
= Laboratoire de Chimie Quantique
Universit=E9 de Strasbourg
PostDoc Supervisor - Dr. Emmanuel Fromager

On Wed, Feb 4, 2015 at 2:56 PM, Kaushik Hatu= a kaushikhatua|*|yahoo.in <owner-che= mistry###ccl.net> wrote:
For = CASSCF you can see the example in g09 website first. Since you confirmed th= e intermediate as biradical then a minimum active space 2,2 is needed. Actu= ally it's very difficult to say. Active space selection is not straight= forward. Where is the two unpaired electron, which orbital they reside all = this are necessary. One black box technique can be adapted where all valenc= e electrons are included in the active space. If the system is big then it = would be time consuming.

Sent from Nokia Lumia

-----Original Message-----
> From: "Rana, Anup rana[a]chemie.uni-siegen.de" <owner-chemistry+/-ccl.net>
Sent: 03-02-2015 06:05 AM
To: "Hatua, Kaushik " <kaushikhatua+/-yahoo.in>
Subject: CCL: Help needed for CASSCF computation either in g09 or in NWChem=


Sent to CCL by: "Rana, Anup" [rana*|*chemie.uni-siegen.de]
Hi all,

Recently I performed one reaction and when I did DFT computation, I found t= hat the reaction is following a stepwise path involving biradical intermedi= ate. So far I know from literature that CASSCF can treat all those multiref= erence problems very well. I have never done CASSCF computation and that is= why I am worried about that. It would be really nice if someone suggest me= , step by step, how to do this computation either in g09 or in NWChem. I am= not a theoretician and that is why a clear technical aspect would be reall= y great for me.

Thank you very much in advance.

With best regards,
Anup Rana



-=3D This is automatically added to each message by the mailing script =3D-= http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubs= cribe/Unsubscribe: Job: http://www.ccl.net/jobs http://www.ccl.net/spammers.tx= t--_1BFEA483-BEDE-4B22-9F0D-828A16B0EF11_
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<html><head><meta http-equiv=3D"Content-Type" cont= ent=3D"text/html; charset=3Dutf-8"></head><body>&l= t;div><div style=3D"font-family: Calibri,sans-serif; font-size: = 11pt;">For CASSCF you can see the example in g09 website first. Sin= ce you confirmed the intermediate as biradical then a minimum active space = 2,2 is needed. Actually it's very difficult to say. Active space select= ion is not straightforward. Where is the two unpaired electron, which orbit= al they reside all this are necessary. One black box technique can be adapt= ed where all valence electrons are included in the active space. If the sys= tem is big then it would be time consuming.<br><br>Sent from No= kia Lumia </div></div><div dir=3D"ltr"><hr&g= t;<span style=3D"font-family: Calibri,sans-serif; font-size: 11pt; = font-weight: bold;">From: </span><span style=3D"font-= family: Calibri,sans-serif; font-size: 11pt;"><a href=3D"ma= ilto:owner-chemistry+/-ccl.net">Rana, Anup rana[a]<= a href=3D"http://chemie.uni-siegen.de" target=3D"_blank">chemie.uni-siegen.= de</a></span><br><span style=3D"font-family: = Calibri,sans-serif; font-size: 11pt; font-weight: bold;">Sent: <= /span><span style=3D"font-family: Calibri,sans-serif; font-size:= 11pt;">03-02-2015 06:05 AM</span><br><span style=3D= "font-family: Calibri,sans-serif; font-size: 11pt; font-weight: bold;&= quot;>To: </span><span style=3D"font-family: Calibri,sans-= serif; font-size: 11pt;"><a href=3D"mailto:kaushikhatua+/-yahoo.in">Hatua, Kaushik </a></span><br= ><span style=3D"font-family: Calibri,sans-serif; font-size: 11pt= ; font-weight: bold;">Subject: </span><span style=3D"= font-family: Calibri,sans-serif; font-size: 11pt;">CCL: Help needed= for CASSCF computation either in g09 or in NWChem</span><br>&l= t;br></div><br>Sent to CCL by: "Rana, Anup" [rana*= |*chemie.uni-sieg= en.de]<br>Hi all,<br><br>Recently I performed one rea= ction and when I did DFT computation, I found that the reaction is followin= g a stepwise path involving biradical intermediate. So far I know from lite= rature that CASSCF can treat all those multireference problems very well. I= have never done CASSCF computation and that is why I am worried about that= . It would be really nice if someone suggest me, step by step, how to do th= is computation either in g09 or in NWChem. I am not a theoretician and that= is why a clear technical aspect would be really great for me.<br><= ;br>Thank you very much in advance.<br><br>With best regards= ,<br>Anup Rana<br><br><br><br>-=3D This is au= tomatically added to each message by the mailing script =3D-<br><b= r<br><br>&= lt;br>E-mail to subscribers: CHEMISTRY+/-ccl.net or use:<br>&nbsp;&nbsp;&nbsp;&a= mp;nbsp;&nbsp; http://www.ccl.net/cgi-bin/ccl/send_ccl_message&l= t;br><br>E-mail to administrators: CHEMISTRY-REQUEST+/-ccl.net or use<br>&nbsp;&am= p;nbsp;&nbsp;&nbsp;&nbsp; http://www.ccl.net/cgi-bin/ccl/sen= d_ccl_message<br><br<br>&nbsp;&nbsp;&nbsp;&a= mp;nbsp;&nbsp;<br><br<br><br>Job: http://www.ccl.net/jobs <br>= ;Conferences: http://server.ccl.net/chemistry/announcements/c= onferences/<br><br>Search Messages: http://www.ccl.ne= t/chemistry/searchccl/index.shtml<br><br>If your mail bounc= es from CCL with 5.7.1 error, check:<br>&nbsp;&nbsp;&nbsp= ;&nbsp;&nbsp;<br><br<br><br><br></bod= y></html>

--001a11342f08a2490f050e445e36-- From owner-chemistry@ccl.net Wed Feb 4 13:17:00 2015 From: "Wendy A Warr wendy|a|warr.com" To: CCL Subject: CCL: Read about drug discovery, text mining, chemical info Message-Id: <-50998-150204123406-21958-9TmMKF1By5VFzWHVWrPAjw ~~ server.ccl.net> X-Original-From: "Wendy A Warr" Date: Wed, 4 Feb 2015 12:34:05 -0500 Sent to CCL by: "Wendy A Warr" [wendy*|*warr.com] Chemical Information and Computation 2014, Number Two. 248th ACS National Meeting and Exposition, San Francisco, CA, August 10-14, 2014 We are pleased to announce the publication later this week of our 44th report in this series. It covers a selection of papers, in detail, from the following technical symposia: Drug Discovery (COMP symposia on ADME/Tox, informatics and ligand-based drug design) Hunting for Hidden Treasures: Chemistry Text Mining in Patents and Other Documents Herman Skolnik Award Symposium 2014 Honoring Engelbert Zass There is also the usual news section covering people, awards, and 65 organizations. The report is over 200 pages long, in full color. Contents list and order forms at http://www.warr.com. Wendy Dr Wendy A. Warr Wendy Warr & Associates