From owner-chemistry&$at$&ccl.net Thu Jun 10 19:22:01 2021 From: "Thomas Manz tmanz|nmsu.edu" To: CCL Subject: CCL: MM/MD program for Windows PC Message-Id: <-54388-210610165133-17607-EyKEL0Uy92B9fDZaKfwoew_._server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary="000000000000c93ec505c46f8d3f" Date: Thu, 10 Jun 2021 14:51:12 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [tmanz###nmsu.edu] --000000000000c93ec505c46f8d3f Content-Type: text/plain; charset="UTF-8" Hi Joe, Some of the Nanohub.org interactive modules/tools may be interesting to check out. These have a graphical user interface (GUI) where users can select computational parameters. The calculation is then run on a backend cluster at Nanohub, and the results are brought back into the GUI and displayed to the user. Everything is done through a web browser with no need to install software, and it runs in real time. The user does not need to supply any computational resources, because the Nanohub cluster runs the simulation. It is free to use. They have a lot of different kinds of modules/tools that relate to various aspects of nanochemistry. Sincerely, Thomas Manz, PhD Associate Professor tmanz:-:nmsu.edu http://wordpress.nmsu.edu/tmanz/ New Mexico State University Department of Chemical & Materials Engineering On Thu, Jun 10, 2021 at 2:40 PM Joseph Leonard jleonard42!A!gmail.com < owner-chemistry:-:ccl.net> wrote: > You might want to look at the educational offerings from Wavefunction ( > www.wavefun.com). They also wrote experimental books as I recall. > > Joe Leonard > > On Thu, Jun 10, 2021 at 2:04 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>>> >>> >>> -- > -- > "Peter Thiel was right, we just can't build cool sh*t anymore. I really > did want a flying car, and all I have is 140 characters and promises of AI > that never come true." > --000000000000c93ec505c46f8d3f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Joe,

Some of the Nanohub.org in= teractive modules/tools may be interesting to check out. These have a graph= ical user interface (GUI) where users can select computational parameters. = The calculation is then run on a backend cluster at Nanohub, and the result= s are brought back into the GUI and displayed to the user. Everything is do= ne through a web browser with no need to install software, and it runs in r= eal time. The user does not need to supply any computational=C2=A0resources= , because the Nanohub cluster runs the simulation. It is free to use. They = have a lot of different kinds of modules/tools that relate to various aspec= ts of nanochemistry.

Sincerely,

Thomas Manz, PhD

Associate Professor

tmanz:-:nms= u.edu

http://wordpress.n= msu.edu/tmanz/

New Mexico State University

Department of Chemical & Materials=C2=A0Engineering


On Thu, Jun 10, 2021 at 2:40 PM Joseph = Leonard jleonard42!A!gmail.com <owner-chemistry:-:ccl.net> wrote:<= br>
You might want to look at the educational offerings from Wavefunction (www.wavefun.com).=C2= =A0 They also wrote experimental books as I recall.
=
Joe Leonard=C2=A0

On Thu, Jun 10, 2021 at 2= :04 PM 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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"Peter Thiel was right, we just can't build cool sh*t anymore. = I really did want a flying car, and all I have is 140 characters and promis= es of AI that never come true."
--000000000000c93ec505c46f8d3f--