From owner-chemistry@ccl.net Thu Mar 14 02:44:00 2019 From: "Pezhman Zarabadi-Poor pzarabadip^-^gmail.com" To: CCL Subject: CCL: Diffusion constants of gas in a MOF using LAMMPS Message-Id: <-53646-190314024237-23945-EYqXH5q29MT+r7VVkf+EGQ]^[server.ccl.net> X-Original-From: Pezhman Zarabadi-Poor Content-Type: multipart/alternative; boundary="0000000000000159040584083aff" Date: Thu, 14 Mar 2019 07:42:18 +0100 MIME-Version: 1.0 Sent to CCL by: Pezhman Zarabadi-Poor [pzarabadip:+:gmail.com] --0000000000000159040584083aff Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Julian, I recommend you to use the following codes for creating the input for your calculations: 1- lammps_interface: https://github.com/peteboyd/lammps_interface 2- OCTP: https://github.com/omoultosEthTuDelft/OCTP Briefly, the first one would help you in setting up the input/data file for the calculations. The latter one requires you to recompile the LAMMPS again to have extra compute and fix options. It will enable using OrderN algorithm for extracting diffusion constants from your calculation results. Cheers, Pezhman On Thu, Mar 14, 2019 at 1:00 AM Julian Umeh cumeh91,,yahoo.com < owner-chemistry(!)ccl.net> wrote: > > Sent to CCL by: "Julian Umeh" [cumeh91^yahoo.com] > I am currently trying to do a simulation of the calculation of diffusion > coefficients of gas in a MOF using LAMMPS. I would appreciate it if anyon= e > who has done something similar send me an input file that I could use as = a > template for the simulation. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Pezhman Zarabadi-Poor, PhDMarie Sk=C5=82odowska-Curie Fellow CEITEC =E2=80=93 Central European Institute of Technology Masaryk University Kamenice 5 Brno Czechia Google Scholar Profile --0000000000000159040584083aff Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Julian,=C2=A0
<= br>
I recommend you to use the following codes for creating the i= nput for your calculations:


Briefly, the first one would help you in s= etting up the input/data file for the calculations. The latter one requires= you to recompile the LAMMPS again to have extra compute and fix options. I= t will enable using OrderN algorithm for extracting diffusion constants fro= m your calculation results.=C2=A0

Cheers,
Pezhman

On Thu, Mar 14, 2019 at 1:00 AM Julian Umeh cume= h91,,yahoo.com <owner-chemistry(!)ccl.net> wrote:

Sent to CCL by: "Julian=C2=A0 Umeh" [cumeh91^yahoo.com]
I am currently trying to do a simulation of the calculation of diffusion coefficients of gas in a MOF using LAMMPS. I would appreciate it if anyone =
who has done something similar send me an input file that I could use as a =
template for the simulation.



-=3D This is automatically added to each message by the mailing script =3D-=
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--

=09 =09 =09 =09

=09 =09 =09 =09

Pezhman Zarabadi-Poor, PhD

Marie Sk=C5=82odowska-Curie Fellow
CEIT= EC =E2=80=93 Central European Institute of Technology
Masaryk University
Kamenice 5=C2=A0
Brno
Czechia

Google Scholar Profile=C2=A0=

--0000000000000159040584083aff-- From owner-chemistry@ccl.net Thu Mar 14 10:25:00 2019 From: "Frank Neese Frank.Neese]_[kofo.mpg.de" To: CCL Subject: CCL: Abstract submission deadline extended for MQM19 Message-Id: <-53647-190314102316-2111-ndv3qeih0h67/N+8t+b8AA**server.ccl.net> X-Original-From: "Frank Neese" Date: Thu, 14 Mar 2019 10:23:11 -0400 Sent to CCL by: "Frank Neese" [Frank.Neese!A!kofo.mpg.de] Dear CCL'ers Due to numerous requests, we have extended the registration deadline for abstracts for the 9th Molecular Quantum Mechanics Conference in Heidelberg to March 31, 2019. Interested parties are requested to submit their abstracts for a talk and/or poster within the next few days so that the conference program can be completed by the beginning of April. The registration deadline for participants will also be extended and we recommend that you register for this conference highlight no later than April when the final program is announced. The 9th MQM 2019 will take place from 30 June to 5 July 2019 in Heidelberg at the Kongresshaus Stadthalle. The Molecular Quantum Mechanics conferences are held as triannual event and offer an overview of current trends and developments in the field of molecular quantum mechanics with a focus on wave function theory. You are invited to come to Heidelberg for discussion and networking with leading scientists in theoretical chemistry! Registration and call for abstracts can be found here mqm2019.org I hope to see many of you in Heidelberg later this year! Best regards, Frank Neese on behalf of the organizing committee From owner-chemistry@ccl.net Thu Mar 14 10:59:00 2019 From: "Grigoriy Zhurko reg_zhurko!^!chemcraftprog.com" To: CCL Subject: CCL: =?windows-1250?Q?=93Survivorship_bias=94_in_science_and_the_Marcel_Swart_DFT_poll?= Message-Id: <-53648-190313151903-30402-Di1I+8Anm2/SXI9YQDucXw{}server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1250 Date: Wed, 13 Mar 2019 22:23:09 +0400 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko*_*chemcraftprog.com] I have heard that the science nowadays experiences a crisis related to the reproduction of previous results: https://arstechnica.com/science/2018/08/why-do-only-two-thirds-of-famous-social-science-results-replicate-its-complicated/ For example, a study in 2015 was made in the field of psychology, which showed than only one third of previous research results in psychology could be replicated. This problem is related to the “Survivorship bias”: https://en.wikipedia.org/wiki/Survivorship_bias Quantum chemists often encounter this problem. If a chemist has computed some properties and got the agreement with the experiment, his results are “publishable”, so he is able to publish it in a reviewed journal. At the same time, if the results of his computation disagree with the experiment, he often has to abandon his results. So, when a DFT functional review is based on a citation analysis, this review is usually biased as noted above. The way to avoid the survivorship bias in chemistry is to significantly take into account the negative results together with the positive ones. There is an analogy with a video on Youtube: it is evidently good that the youtube users are able to put dislikes along with the likes, and I could show some video clips which illustrate that the ratio between the number of likes and the number of dislikes is often a much better indicator of the clip quality, than the number of likes or the number of views. As far as I know, at the moment only the Marcel Swart DFT poll is a kind of research on the reliability of DFT functionals, which is based on using negative results (“dislikes”) together with the positive results (“likes”). That’s why I think that the community should support the work of Mr. Swart, although he should make it more rigorous (I wrote some details about this earlier). From owner-chemistry@ccl.net Thu Mar 14 11:34:00 2019 From: "Harald Lanig harald.lanig|-|fau.de" To: CCL Subject: CCL: [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany Message-Id: <-53649-190314034459-16230-LMh7cOshsfzOtwrUoSnr0w- -server.ccl.net> X-Original-From: Harald Lanig Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8"; format=flowed Date: Thu, 14 Mar 2019 08:44:51 +0100 MIME-Version: 1.0 Sent to CCL by: Harald Lanig [harald.lanig*fau.de] Dear list subscribers, we are very delighted to remind you about this year’s “33rd Molecular Modelling Workshop (MMWS)” (http://mmws2019.mgms-ds.de) that takes place on April, Monday 8th to Wednesday 10th, 2019, at the Friedrich-Alexander-University in Erlangen, Germany. Please notice that registration is still possible until March 22nd, 2019! The MMWS has a long history of giving young scientists (especially graduate students) the opportunity to present their work and dive into discussions with each other and the "older experts" of the field to gain valuable feedback from academic as well as industrial colleagues. Oral and poster contributions are welcome from all areas of molecular modelling – from the life sciences, computational biology and chemistry, cheminformatics, to materials sciences. Starting with the scientific program on Monday after lunch should allow to avoid travelling on weekend keeping the expenses at a minimum. A hearty workshop dinner and a traditional joint evening in Erlangen’s Steinbach-Bräu brewery complement the scientific program. The workshop is organised by the German Section of the Molecular Graphics and Modelling Society (MGMS-DS e.V.). ####### Satellite symposium in honour of Tim Clark's 70th birthday ####### Directly after the MMWS, there will be a one-day symposium on Thursday April 11th, 2019 to celebrate the occasion of Tim Clark's 70th birthday. You are invited to attend this meeting and extend your stay in Erlangen by an extra day. There will be invited lectures only and no contributed talks. There is no registration, conference desk, or extra fee. Nevertheless, we expect that you indicate your interest in attending on Thursday by checking the corresponding field during registration for the MMWS. For further information about our Birthday Symposium, please refer to "Tim-Clark-Day" via https://mmws2019.mgms-ds.de/index.php?m=113 ####### Pre-conference workshop ####### For the second time at our Molecular Modeling Workshop, Schrödinger is offering a pre-conference workshop entiteled "Structure-based Drug Design using the Schrödinger Suite". If you are interested in participating at the software session, please checkmark the corresponding field upon filling the registration form. ####### Plenary Speakers ####### We are very happy to announce that four outstanding researchers accepted our invitation to present a plenary lecture at the Modeling workshop: Matthias Bremer (Merck KGaA, Darmstadt) "The Role of Quantum Chemistry in the Development of Liquid Crystals for Display Applications" Ruth Brenk (University of Bergen) "Structure-based design of riboswitch ligands and selective NMT inhibitors" Bernd Meyer (University of Erlangen) "Chemistry at the solid-liquid interface" Rochus Schmid (Ruhr-University Bochum) "Force fields for porous coordination polymers - a tricky business" ####### Poster and Lecture Awards ####### As in the past years, there will be two poster awards of EUR 100 each and three lecture awards for the best contributed oral presentations: 1st winner: Travel bursary to attend the Young Modeller's Forum in London, UK, plus a speaker slot option at YMF (travel expenses are reimbursed up to EUR 500) 2nd winner: EUR 200 travel expenses reimbursement 3rd winner: EUR 100 travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. ####### Registration and poster/talk submission ####### Submit talks and/or poster titles via the registration form accessible on the workshop website https://mmws2019.mgms-ds.de/index.php?m=register The deadline for all submissions is March 22nd, 2019. ####### General information ####### Website http://mmws2019.mgms-ds.de will provide all necessary information about the meeting. We are looking forward to meeting you in Erlangen! - Paul Czodrowski, Scientific Committee Workshop Organisation 2019 - Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.de) -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen Fon +49 9131-85 20781 harald.lanig[-]fau.de Fax +49 9131-85 20785 http://www.zisc.uni-erlangen.de ------------------------------------------------------------------------ From owner-chemistry@ccl.net Thu Mar 14 15:08:00 2019 From: "Lehtola, Susi susi.lehtola=-=helsinki.fi" To: CCL Subject: CCL: =?windows-1250?Q?Re:_CCL:_=93Survivorship_bias=94_in_science_and_the_Marc?= =?windows-1250?Q?el_Swart_DFT_poll?= Message-Id: <-53650-190314134823-19373-WPWx1/ehrTD+y4VPnCLilQ ~ server.ccl.net> X-Original-From: "Lehtola, Susi" Content-ID: <1D54A201D35E3449AF3F00EF281D322A ~ eurprd07.prod.outlook.com> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="windows-1250" Date: Thu, 14 Mar 2019 17:48:15 +0000 MIME-Version: 1.0 Sent to CCL by: "Lehtola, Susi" [susi.lehtola###helsinki.fi] On 3/13/19 8:23 PM, Grigoriy Zhurko reg_zhurko!^!chemcraftprog.com wrote: > > Sent to CCL by: Grigoriy Zhurko [reg_zhurko*_*chemcraftprog.com] > > > I have heard that the science nowadays experiences a crisis related > to the reproduction of previous results: > > https://arstechnica.com/science/2018/08/why-do-only-two-thirds-of-famous-social-science-results-replicate-its-complicated/ > > For example, a study in 2015 was made in the field of psychology, > which showed than only one third of previous research results in > psychology could be replicated. > > This problem is related to the “Survivorship bias”: > > https://en.wikipedia.org/wiki/Survivorship_bias > > Quantum chemists often encounter this problem. If a chemist has > computed some properties and got the agreement with the experiment, > his results are “publishable”, so he is able to publish it in a > reviewed journal. At the same time, if the results of his computation > disagree with the experiment, he often has to abandon his results. > So, when a DFT functional review is based on a citation analysis, > this review is usually biased as noted above. There *are* density functional reviews based on actual accuracy data, see e.g. doi:10.1080/00268976.2017.1333644 > The way to avoid the survivorship bias in chemistry is to > significantly take into account the negative results together with > the positive ones. There is an analogy with a video on Youtube: it > is evidently good that the youtube users are able to put dislikes > along with the likes, and I could show some video clips which > illustrate that the ratio between the number of likes and the number > of dislikes is often a much better indicator of the clip quality, > than the number of likes or the number of views. As far as I know, at > the moment only the Marcel Swart DFT poll is a kind of research on > the reliability of DFT functionals, which is based on using negative > results (“dislikes”) together with the positive results (“likes”). > That’s why I think that the community should support the work of Mr. > Swart, although he should make it more rigorous (I wrote some details > about this earlier). But since there are way more users than developers, the poll is biased since most users have heard of any new functionals since PBE or B3LYP, and survivor bias is even more inherent among the users! For instance, the winners of the poll from 2010 to 2017 show astounding variety: PBE0, PBE0, PBE, PBE, PBE, PBE, PBE, PBE0 Goerigk and Mehta write in their recent paper: "It is striking that even in the 2017 poll one third of the first-division methods belong to the 16 worst DFA approaches for GMTKN55!" For more discussion on the DFT poll, see the paper "A Trip to the Density Functional Theory Zoo: Warnings and Recommendations for the User", doi:10.1071/CH19023. (No, I don't want to start yet another flame war on the poll.) -- ------------------------------------------------------------------ Mr. Susi Lehtola, PhD Junior Fellow, Adjunct Professor susi.lehtola+/-helsinki.fi University of Helsinki http://susilehtola.github.io/ Finland ------------------------------------------------------------------ Susi Lehtola, dosentti, FT tutkijatohtori susi.lehtola+/-helsinki.fi Helsingin yliopisto http://susilehtola.github.io/ ------------------------------------------------------------------