From owner-chemistry _-at-_)ccl.net Fri Jun 11 15:42:00 2021 From: "Anatoli Korkin korkin*_*nanoandgiga.com" To: CCL Subject: CCL: MM/MD program for Windows PC Message-Id: <-54394-210611153936-28703-V9PMNUAYsk2lSPym5LBPtQ%server.ccl.net> X-Original-From: Anatoli Korkin Content-Type: multipart/alternative; boundary="0000000000008d522e05c482aa61" Date: Fri, 11 Jun 2021 14:39:18 -0500 MIME-Version: 1.0 Sent to CCL by: Anatoli Korkin [korkin!^!nanoandgiga.com] --0000000000008d522e05c482aa61 Content-Type: text/plain; charset="UTF-8" Thank you very much, Brian! Next-Generation Molecular Workbench is really useful instrument for simple illustration of physics, chemistry and biology and I added in a collection of the lessons on my youtube channel: https://www.youtube.com/watch?v=pavnxcgKGhg I also installed LAMMPS executables on my Windows PC but may take some times for me to learn it myself and to generate a (relatively) simple algorithm of generating some lessons which high school students or at least teachers can use. If someone who reads this message is LAMMPS experts and is willing to help, it would be great! Best regards, Anatoli Korkin Tel: +1-480-329-5710 (WhatsApp, Viber, Telegram and WeChat); Skype: anatolik51 Adjunct Professor School of Molecular Sciences Arizona State University webapp4.asu.edu/directory/person/1169125 President of Nano and Giga Solutions Inc. nanoandgiga.com/board/korkin.html On Thu, Jun 10, 2021 at 5:59 PM Brian Skinn brian.skinn : gmail.com < owner-chemistry_-_ccl.net> wrote: > Anatoli, > > I did a quick Google search for "interactive molecular model of > condensation", and discovered this: http://mw.concord.org/nextgen/ > > I have no experience with them at all, and cannot make any particular > recommendation. The demonstration on the landing page seems exactly like > what you describe, though. I'm not sure how you would go about making use > of their product...it might involve becoming one of their "partners"? > > > Good luck, > Brian > > On Thu, Jun 10, 2021 at 3:30 PM Anatoli Korkin korkin.{}.nanoandgiga.com < > owner-chemistry{}ccl.net> wrote: > >> I need something which students and teachers with no professional >> chemistry background could use as demo lessons of "virtual chemistry". Like >> a virtual lab. The best analogy is chemistry demonstration in the class by >> mixing some liquids with a visual result: color change, gas or sediment, >> etc. In this case the visual effects would be conformation changes or >> formation of a molecular cluster (temperature down) or cluster evaporation >> (temperature up). There are plenty movies on youtube of any level of >> complexity but they would not provide a hands-on experience and ability to >> change some parameters to get feeling of doing a "chemistry experiment". >> >> Best regards, >> Anatoli Korkin >> Adjunct Professor >> School of Molecular Sciences >> Arizona State University >> webapp4.asu.edu/directory/person/1169125 >> President of Nano and Giga Solutions Inc. >> nanoandgiga.com/board/korkin.html >> >> >> >> On Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=}cgl.ucsf.edu < >> owner-chemistry#%#ccl.net> wrote: >> >>> >>> Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu] >>> If this is for noncommercial use, you could take a look at the Sophia >>> plugin to UCSF Chimera; both are free downloads for noncommercial purposes: >>> >>> https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#sophia >>> https://sophia-web.appspot.com/ >>> https://www.rbvi.ucsf.edu/chimera/index.html >>> >>> However, Sophia may be intended more to teach principles of MD using >>> simple systems, than to teach chemistry per se. Also developed mainly for >>> Mac although documentation says most features also work on Windows, and >>> while it may be easy for you to install, not necessarily so for students. >>> >>> Best, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>> > On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.com >>> wrote: >>> > >>> > >>> > Sent to CCL by: "Anatoli Korkin" [korkin^nanoandgiga.com] >>> > I am looking for a free MM/MD program easy to install and operate in >>> Windows PC >>> > environment to design some chemistry lessons for high school students, >>> e.g. >>> > conformational changes and condensation/evaporation with temperature >>> change. >>> > Even better if someone, who is expert in MM/MD, would be interested to >>> join the >>> > project and develop some video lessons. See examples on my youtube >>> channel >>> > "Atomic Scale Design for Newbies": >>> > >>> > https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA >>> > >>> > Thank you for your advice and consideration! >>> > >>> > Sincerely, >>> > Anatoli Korkin>>> E-mail to subscribers: CHEMISTRY#%#ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST#%#ccl.net or use>>> >>> >>> --0000000000008d522e05c482aa61 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thank you very much, Brian!

Next-Generation Molecular Workbench is really useful instr= ument for simple illustration of physics, chemistry and biology and I added= in a collection of the lessons on my youtube=C2=A0channel:

<= /div>

I a= lso installed LAMMPS executables on my Windows PC but may take some times f= or me to learn it myself=C2=A0and to generate a (relatively) simple algorit= hm of generating some lessons which high school students or at least teache= rs can use. If someone who reads this message is LAMMPS experts and is will= ing to help, it would be great!=C2=A0=C2=A0

=
Best regard= s,
Anatoli Korkin
Tel: +1-48= 0-329-5710 (WhatsApp, Viber, Telegram and WeChat); =C2=A0Skype: anatolik51
Adjunct Professor
School of Molecular S= ciences
Arizona State University
President of Nano and Giga Solutio= ns Inc.

=


On Thu, Jun 10, 2021 at 5:59 PM Bri= an Skinn brian.skinn : gmail.com <owner-chemistry_-_ccl.net> wrote= :
Anatoli,

I did a quick Google search for "intera= ctive molecular model of condensation", and discovered this:=C2=A0http://mw.concord.= org/nextgen/

I have no experience with them at= all, and cannot make any particular recommendation. The demonstration on t= he landing page seems exactly like what you describe, though. I'm not s= ure how you would go about making use of their product...it might involve b= ecoming=C2=A0one of their "partners"?

Good luck,
Brian

On Thu, Jun 10, 2021 at 3:30 P= M Anatoli Korkin korkin.{}.nanoandgiga.com <owner-chemistry{}ccl.net> wrote:
I need so= mething which students and teachers with no professional chemistry backgrou= nd could use as demo lessons of "virtual chemistry". Like a virtu= al lab. The best analogy is chemistry demonstration in the class by mixing = some liquids with a visual result: color change, gas or sediment, etc. In t= his case the visual effects would be conformation changes or formation of a= molecular cluster (temperature down) or cluster evaporation (temperature u= p). There are plenty movies on youtube of any level of complexity but they = would not provide a hands-on experience and ability to change some paramete= rs=C2=A0to get feeling of doing a "chemistry experiment".
Best regards,
Anatoli Korkin
Adjunct Professor
School= of Molecular Sciences
Arizona State University
President of Nano a= nd Giga Solutions Inc.



On Wed, Jun 9, 2021 = at 7:48 PM Elaine Meng meng{=3D}cgl.ucsf.edu <owner-chemistry#%#ccl.net> wrote:

Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu]
If this is for noncommercial use, you could take a look at the Sophia plugi= n to UCSF Chimera; both are free downloads for noncommercial purposes:

https://www.rbvi.ucsf.edu/chimera/plugi= ns/plugins.html#sophia
https://sophia-web.appspot.com/
https://www.rbvi.ucsf.edu/chimera/index.html

However, Sophia may be intended more to teach principles of MD using simple= systems, than to teach chemistry per se.=C2=A0 Also developed mainly for M= ac although documentation says most features also work on Windows, and whil= e it may be easy for you to install, not necessarily so for students.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.= com <owner-chemistry~!~ccl.net> wrote:
>
>
> Sent to CCL by: "Anatoli=C2=A0 Korkin" [korkin^nanoandgiga.com<= /a>]
> I am looking for a free MM/MD program easy to install and operate in W= indows PC
> environment to design some chemistry lessons for high school students,= e.g.
> conformational changes and condensation/evaporation with temperature c= hange.
> Even better if someone, who is expert in MM/MD, would be interested to= join the
> project and develop some video lessons. See examples on my youtube cha= nnel
> "Atomic Scale Design for Newbies":
>
> https://www.youtube.com/channel/UCQZL1U= yyBo7HuN-FA286YWA
>
> Thank you for your advice and consideration!
>
> Sincerely,
> Anatoli Korkin



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