From owner-chemistry@ccl.net Tue Oct 20 01:34:00 2020 From: "Cheol Ho Choi cheolho.choi]*[gmail.com" To: CCL Subject: CCL: Webinar: New Horizons in Scientific Software Message-Id: <-54191-201020002531-9956-MuaDzMIs7QHSJJYYALGEcw{=}server.ccl.net> X-Original-From: "Cheol Ho Choi" Date: Tue, 20 Oct 2020 00:25:30 -0400 Sent to CCL by: "Cheol Ho Choi" [cheolho.choi^gmail.com] "New Horizons in Scientific Software: from Legacy Codes to Modular Environments" (https://www.edison.re.kr/web/nhiss/) It is our great pleasure to invite you to participate in the web conference taking place > from Nov 23 to Nov 26, 2020. This is the first conference in a series dedicated to the development and application of modular computational platform for the general science and technology community. As the old-fashioned approach to developing and maintaining computational programs becomes obsolete, an emerging concept of software modularity offers an elegant and timely solution of the looming problems by providing an open development ecosystem where new computational approaches can be rapidly created from modules uploaded at the web repository by the interested users and developers. We have more than 20 world renowned speakers such as Prof. Mark Gordon (ISU), T. Daniel Crawford (Virginia Tech.), Massimo Olivucci (University of Siena), Garnet Chan (Caltech) and others, who are actively developing the most popular quantum mechanical softwares, such as GAMESS, Psi4, pySCF, Molcas, Columbus, Newton-X, DCDFTBMD, Gellan, Libint, etc. A free registration is now open as a first-come-first-serve basis with the limit of 500 participants at https://us02web.zoom.us/webinar/register/WN_B9-QFW89S-OZr0e-EzpfQw?timezone_id=UTC With the best regards, Cheol Ho Choi Department of Chemistry, Kyungpook National University, South Korea http://qchem.knu.ac.kr, Email: cheolho.choi^^^gmail.com With the organizing committee of Dr. Jeong Hyeon Seo at the Korea Institute of Science and Technology Information (KISTI) https://www.kisti.re.kr Email: jerryhseo^^^gmail.com Prof. Michael Filatov at the Department of Chemistry, Kyungpook National University, South Korea Email: mike.filatov^^^gmail.com From owner-chemistry@ccl.net Tue Oct 20 12:36:00 2020 From: "Lance Westerhoff lance^_^mac.com" To: CCL Subject: CCL: Torsion space forcefield minimization Message-Id: <-54192-201020113839-30881-bU/5T+zH9tRIgPCPd1Nphw#%#server.ccl.net> X-Original-From: Lance Westerhoff Content-Type: multipart/alternative; boundary="Apple-Mail=_7797AB96-4A72-4DE6-BA02-57EE25785EFB" Date: Tue, 20 Oct 2020 11:38:30 -0400 Mime-Version: 1.0 (Mac OS X Mail 11.5 \(3445.9.1\)) Sent to CCL by: Lance Westerhoff [lance\a/mac.com] --Apple-Mail=_7797AB96-4A72-4DE6-BA02-57EE25785EFB Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Joe- DivCon (qmechanic) is able to perform torsion-only optimization. We = implemented it with linear scaling QM (SE: pm6, etc), MM (amber/gaff), = and QM/MM and it can be done with or without experimental density. = It=E2=80=99s really fast which makes it a benefit vs. all atom = approaches. Unfortunately, I=E2=80=99m not aware of any opensource apps that do it = since we wrote our torsion opt from scratch. Certainly, let me know if = you=E2=80=99d like to give it a try! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. Calendar: https://calendly.com/lwesterhoff = WWW: http://www.quantumbioinc.com Email: lance:-:quantumbioinc.com Cell: 814-574-0221 Fax: 814-235-6909 This message and any attachments are solely for the intended recipient = and should be considered confidential. If you are not the intended = recipient, please immediately and permanently delete. > On Oct 17, 2020, at 11:20 AM, Joseph Leonard jleonard42+*+gmail.com = > wrote: >=20 > Folks, is anybody aware of a program that offers torsion-space = minimization (no bond length/angle change) of one or two/paired = molecules? I was aware of commercial offerings they did this long ago = and I wondered whether it have become (more) available. Pointers = welcome! >=20 > Joe Leonard > --=20 > -- > But if biology were the reason so few women are in coding, it would be = impossible to explain why women were so prominent in the early years of = American programming, when the work could be, if anything, far harder = than today=E2=80=99s programming. It was an uncharted new field, in = which you had to do math in binary and hexadecimal formats, and there = were no helpful internet forums, no Google to query, for assistance with = your bug. It was just your brain in a jar, solving hellish problems. --Apple-Mail=_7797AB96-4A72-4DE6-BA02-57EE25785EFB Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8

Hi Joe-

DivCon (qmechanic) is able to perform torsion-only = optimization. We implemented it with linear scaling QM (SE: pm6, etc), = MM (amber/gaff), and QM/MM and it can be done with or without = experimental density. It=E2=80=99s really fast which makes it a benefit = vs. all atom approaches.

Unfortunately, I=E2=80=99m not aware of any opensource apps = that do it since we wrote our torsion opt from scratch. Certainly, let = me know if you=E2=80=99d like to give it a try!

-Lance
____________________
Lance M. Westerhoff, = Ph.D.
President and General Manager
QuantumBio= Inc.


WWW: http://www.quantumbioinc.com
Email: lance:-:quantumbioinc.com

Cell: 814-574-0221
Fax: = 814-235-6909


This = message and any attachments are solely for the intended recipient = and
should be considered confidential. If you are not = the intended recipient,
please immediately and = permanently delete.



On Oct 17, 2020, at 11:20 AM, Joseph Leonard = jleonard42+*+gmail.com = <owner-chemistry:-:ccl.net> wrote:

Folks, is anybody aware of a program that offers = torsion-space minimization (no bond length/angle change) of one or = two/paired molecules?  I was aware of commercial offerings they did = this long ago and I wondered whether it have become (more) available. = Pointers welcome!

Joe Leonard
--
--
But if biology were the = reason so few women are in coding, it would be impossible to explain why = women were so prominent in the early years of American programming, when = the work could be, if anything, far harder than today=E2=80=99s = programming.  It was an uncharted new field, in which you had to do = math in binary and hexadecimal formats, and there were no helpful = internet forums, no Google to query, for assistance with your bug.  = It was just your brain in a jar, solving hellish = problems.

= --Apple-Mail=_7797AB96-4A72-4DE6-BA02-57EE25785EFB--