From owner-chemistry@ccl.net Tue Jun 9 07:27:00 2015 From: "Jan Boyke Sch nborn boyke.schoenborn_+_uni-potsdam.de" <owner-chemistry|a|server.ccl.net> To: CCL Subject: CCL: STC 2015: Registration is closing soon! Message-Id: <-51432-150609041036-23124-lL7vcbgCHmBj2GbKmqlb9g|a|server.ccl.net> X-Original-From: "Jan Boyke Sch nborn" <boyke.schoenborn+/-uni-potsdam.de> Date: Tue, 9 Jun 2015 04:10:35 -0400 Sent to CCL by: "Jan Boyke Sch nborn" [boyke.schoenborn-,-uni-potsdam.de] Dear CCL subscribers, on behalf of the organizers I'd like to post the following announcement regarding the Symposium on Theoretical Chemistry 2015 in Potsdam. STC 2015 - SECOND ANNOUNCEMENT Dear Colleagues, we would kindly like to remind you that the registration deadline for the 51st Symposium on Theoretical Chemistry is approaching. Please, register until *** June 15, 2015. *** The STC 2015 will take place at the University of Potsdam (Germany) from September 20 to 24, 2015. The registration fee is 250 EUR for regular participants and 200 EUR for doctoral students. It will cover the book of abstracts, the welcome reception on Sunday evening, all coffee breaks and meals, the poster sessions and the conference dinner at Prinz Eisenherz in Filmpark Babelsberg. This year's symposium will feature 13 invited speakers from various fields of theory. In addition, 25 slots for contributed talks and two evening poster sessions are offered for your contribution from any topic of theoretical chemistry. Abstract submission for oral and poster contributions is open until *** June 30, 2015. *** Please note that the contingent of blocked rooms in the close vicinity of the conference site is expiring soon. For more information, visit our conference website at http://www.chem.uni-potsdam.de/stc2015. Hope to see you in Potsdam! The STC 2015 organization committee Peter Saalfrank Tillmann Klamroth Thomas Koerzdoerfer From owner-chemistry@ccl.net Tue Jun 9 09:02:00 2015 From: "Robert Robinson robertr3]*[utas.edu.au" <owner-chemistry**server.ccl.net> To: CCL Subject: CCL: Single-point energy restart Message-Id: <-51433-150609082612-6061-TSV2hu6xlMayg7/XHIT1vQ**server.ccl.net> X-Original-From: "Robert Robinson" <robertr3:utas.edu.au> Date: Tue, 9 Jun 2015 08:26:11 -0400 Sent to CCL by: "Robert Robinson" [robertr3%%utas.edu.au] Dear CCL, Is it possible to restart a single-point energy calculation from the checkpoint file that run-out of wall-time? Robert From owner-chemistry@ccl.net Tue Jun 9 11:35:00 2015 From: "Renier Dreyer renier.dreyer..crunchyard.com" <owner-chemistry_+_server.ccl.net> To: CCL Subject: CCL: ADF 2014.07 now available on CrunchYard HPC Message-Id: <-51434-150609113210-19647-1uz/jOJurGVF/2q5chEdgQ_+_server.ccl.net> X-Original-From: "Renier Dreyer" <renier.dreyer-.-crunchyard.com> Date: Tue, 9 Jun 2015 11:32:08 -0400 Sent to CCL by: "Renier Dreyer" [renier.dreyer%x%crunchyard.com] CrunchYard is pleased to announce ADF 2014.07 is now available online via our HPC platform for users with an ADF license. Access hundreds of cores instantly! The ADF modeling suite consists of powerful DFT codes ADF (molecules) and BAND (surfaces, bulk), a DFTB module, ReaxFF, and COSMO-RS. For optimum usability, a local copy of the excellent GUI is recommended (visit www.scm.com/trial for a free trial). Visit www.crunchyard.com for more or email Dr. Renier Dreyer renier.dreyer_+_crunchyard.com to find out how to activate ADF on your CrunchYard profile. Alternatively contact SCM on how to get started. From owner-chemistry@ccl.net Tue Jun 9 12:09:00 2015 From: "Billy McCann thebillywayne|gmail.com" <owner-chemistry[A]server.ccl.net> To: CCL Subject: CCL: Determine statistical distribution of chemical species based on energi Message-Id: <-51435-150609120543-30680-H3lrtIL6rvBZ2QWnm+nUvA[A]server.ccl.net> X-Original-From: Billy McCann <thebillywayne!=!gmail.com> Content-Type: text/plain; charset=UTF-8 Date: Tue, 9 Jun 2015 12:05:18 -0400 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne(a)gmail.com] >Can you determine theoretical statistical distributions of these states based on energies calculated by DFT or ab initio calculations? Yes. It's quite simple, actually. You'll want to calculate the free energy of the conformers, etc. and then find the Boltzmann distribution. See the above responses for details into partition functions and the rest. Typically your software will calculate these and have them in the output file. https://en.wikipedia.org/wiki/Boltzmann_distribution >Which types of energies would you need? Free energies. Be sure to convert the free energies to the desired standard state. >How would you do it? See equation 10.49 in Cramer's book, Essentials of Computational Chemistry. I was looking at some point in my research to get more precise calculations by finding the Gibb's free energy of an equilibrium population. I wrote a python script to compute the relative populations. It can be found here. https://gist.github.com/thebillywayne/47d77ea6b0e03b245144 Take note that if you have degenerate states, you simply feed them into the script twice. I also have a script that calculates the inverse, that is, starts with the abundances and calculates the free energies. Note that these populations are calculated at 298K. Change the RT variable if you want a different temperature. It's always a little nerve racking to share code with a broad community. But I welcome feedback. -- Billy Wayne McCann, Ph.D. http://bwayne.sdf.org irc://irc.freenode.net:bwayne From owner-chemistry@ccl.net Tue Jun 9 20:40:01 2015 From: "Gustavo L.C. Moura gustavo.moura|a|ufpe.br" <owner-chemistry]![server.ccl.net> To: CCL Subject: CCL: Proper way of doing a Boltzmann average Message-Id: <-51436-150609203805-12713-syM2I3ZlDGcdGmdqzELiPQ]![server.ccl.net> X-Original-From: "Gustavo L.C. Moura" <gustavo.moura]^[ufpe.br> Date: Tue, 9 Jun 2015 20:37:58 -0400 Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura%x%ufpe.br] Dear CCL community, I am seeking advice about the proper way of calculating a Boltzmann average. For the sake of argument, let us say that I have a molecule that may assume only two distinct conformations A and B. I have no problems calculating the Boltzmann averaged property in this case. However, I have strong theoretical and experimental evidences that my molecule forms a hydrogen bonded dimer. The dimerization process does not affect the flexibility of each monomer and they still have the same two conformations A and B as before. I have no problems dealing with the averaging process for the dimers in conformations AA and BB (they are unique). My problem is with conformations AB and BA. The two dimers can be superimposed (and are technically equal), but I still know which monomer has each conformation. My question is: should I include both dimers in the Boltzmann average or should I include only one of them in the Boltzmann average? Your advice is most welcome. Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura