From owner-chemistry@ccl.net Tue May 4 06:20:01 2021 From: "Andrey KALINICHEV kalinich : subatech.in2p3.fr" To: CCL Subject: CCL: How to find data files for experimentally-obtained RDFs of water Message-Id: <-54319-210504061525-1208-qgfM9TNz7d2FiHf7GKNZKQ[]server.ccl.net> X-Original-From: Andrey KALINICHEV Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 4 May 2021 12:15:12 +0200 MIME-Version: 1.0 Sent to CCL by: Andrey KALINICHEV [kalinich+*+subatech.in2p3.fr] Hi, I've just sent you the tabulated experimental RDFs as they were used > from the original sources in my old paper of 1997: Kalinichev, A. G.; Bass, J. D., Hydrogen bonding in supercritical water .2. Computer simulations. Journal of Physical Chemistry A 1997, 101, 9720-9727. Andrey -- Dr. Andrey G. KALINICHEV, Directeur de Recherche SUBATECH (UMR 6457 - IMT Atlantique, Université de Nantes, CNRS/IN2P3) 4 rue Alfred Kastler, La Chantrerie - CS 20722 44307 Nantes Cedex 3, FRANCE Tél: +33 (0)2.51.85.84.80 E-mail: kalinich{at}subatech.in2p3.fr http://www.imt-atlantique.fr/en/person/andrey-kalinichev Le 2021-05-03 à 21:44, Andrew DeYoung andrewdaviddeyoung[*]gmail.com a écrit : > Hi, > > I am mentoring a first-year undergraduate in computational chemistry.  I > am having him run a brief MD simulation of water at 300 K and calculate > the radial distribution functions (RDFs) g_OO(r), g_OH(r), and g_HH(r). > I am not an experimentalist, but I understand that those RDFs can be > obtained from some clever measurements, such as X-ray scattering. > > I would like to have my undergraduate student overlay his RDFs (obtained > from simulation) on top of experimentally-obtained RDFs so that he can > see that even a relatively simple water model such as SPC does a > reasonable job of reproducing the experimental structures.  In the > literature there are lots of papers that make such comparisons between > simulation and experiment, but if possible, I would like my student to > actually plot the comparisons himself. > > Does anyone have any idea where I can find data files for > experimentally-obtained RDFs (i.e., just g_OO(r), g_OH(r), and g_HH(r)) > for water -- short of trying to extract data from plots in literature > paper PDFs, under educational fair use?  Unfortunately, Google did not > seem to help me this time... :-) > > Thanks, > Andrew DeYoung > Carnegie Mellon University > andrewdaviddeyoung AT gmail.com From owner-chemistry@ccl.net Tue May 4 06:54:01 2021 From: "Jacek Korchowiec korchow^-^chemia.uj.edu.pl" To: CCL Subject: CCL: How to find data files for experimentally-obtained RDFs of water Message-Id: <-54320-210504064726-12719-zVhBJnY3NBVFmwxvvX39IA-x-server.ccl.net> X-Original-From: "Jacek Korchowiec" Date: Tue, 4 May 2021 06:47:24 -0400 Sent to CCL by: "Jacek Korchowiec" [korchow:-:chemia.uj.edu.pl] Hello, All the listed RDFs (g_OO, g_OH, and g_HH) for water can be found in the paper of: Soper, A. K. The Radial Distribution Functions of Water as Derived from Radiation Total Scattering Experiments: Is There Anything We Can Say for Sure? ISRN Physical Chemistry 2013 1-67 Best regards, Jacek Korchowiec From owner-chemistry@ccl.net Tue May 4 09:05:00 2021 From: "m.dominic.ryan ~~ gmail.com" To: CCL Subject: CCL: How to find data files for experimentally-obtained RDFs of water Message-Id: <-54321-210503223111-26768-yBTSOfup0n4XbwKEL+jdVQ]![server.ccl.net> X-Original-From: Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_04DB_01D7406B.FBDE09B0" Date: Mon, 3 May 2021 22:30:55 -0400 MIME-Version: 1.0 Sent to CCL by: [m.dominic.ryan-$-gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_04DB_01D7406B.FBDE09B0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Many years ago Bill Jorgensen had developed BOSS, a monte-carlo liquid = simulation, that was aimed at reproducing lots of experimental data such = as densities. I seem to recall RDFs being cited by him. I suggest at = least looking up those old papers but perhaps you could also just email = him at Yale. =20 Dominic =20 > From: owner-chemistry+m.dominic.ryan=3D=3Dgmail.com^-^ccl.net = On Behalf Of = Andrew DeYoung andrewdaviddeyoung[*]gmail.com Sent: Monday, May 3, 2021 3:45 PM To: Ryan, M Dominic Subject: CCL: How to find data files for experimentally-obtained RDFs of = water =20 Hi, =20 I am mentoring a first-year undergraduate in computational chemistry. I = am having him run a brief MD simulation of water at 300 K and calculate = the radial distribution functions (RDFs) g_OO(r), g_OH(r), and g_HH(r). = I am not an experimentalist, but I understand that those RDFs can be = obtained from some clever measurements, such as X-ray scattering. =20 =20 I would like to have my undergraduate student overlay his RDFs (obtained = > from simulation) on top of experimentally-obtained RDFs so that he can = see that even a relatively simple water model such as SPC does a = reasonable job of reproducing the experimental structures. In the = literature there are lots of papers that make such comparisons between = simulation and experiment, but if possible, I would like my student to = actually plot the comparisons himself. =20 Does anyone have any idea where I can find data files for = experimentally-obtained RDFs (i.e., just g_OO(r), g_OH(r), and g_HH(r)) = for water -- short of trying to extract data from plots in literature = paper PDFs, under educational fair use? Unfortunately, Google did not = seem to help me this time... :-) =20 Thanks, Andrew DeYoung Carnegie Mellon University andrewdaviddeyoung AT gmail.com =20 ------=_NextPart_000_04DB_01D7406B.FBDE09B0 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable

Many = years ago Bill Jorgensen had developed BOSS, a monte-carlo liquid = simulation, that was aimed at reproducing lots of experimental data such = as densities. I seem to recall RDFs being cited by him. I suggest at = least looking up those old papers but perhaps you could also just email = him at Yale.

 

Dominic

 

From: = owner-chemistry+m.dominic.ryan=3D=3Dgmail.com^-^ccl.net = <owner-chemistry+m.dominic.ryan=3D=3Dgmail.com^-^ccl.net> On = Behalf Of Andrew DeYoung = andrewdaviddeyoung[*]gmail.com
Sent: Monday, May 3, 2021 3:45 = PM
To: Ryan, M Dominic = <m.dominic.ryan^-^gmail.com>
Subject: CCL: How to find = data files for experimentally-obtained RDFs of = water

 

Hi,

 

I = am mentoring a first-year undergraduate in computational = chemistry.  I am having him run a brief MD simulation of water at = 300 K and calculate the radial distribution functions (RDFs) g_OO(r), = g_OH(r), and g_HH(r).  I am not an experimentalist, but I = understand that those RDFs can be obtained from some clever = measurements, such as X-ray scattering.  =

 

I = would like to have my undergraduate student overlay his RDFs (obtained = > from simulation) on top of experimentally-obtained RDFs so that he can = see that even a relatively simple water model such as SPC does a = reasonable job of reproducing the experimental structures.  In the = literature there are lots of papers that make such comparisons between = simulation and experiment, but if possible, I would like my student to = actually plot the comparisons himself.

 

Does anyone have any idea where I can find data files = for experimentally-obtained RDFs (i.e., just g_OO(r), g_OH(r), and = g_HH(r)) for water -- short of trying to extract data from plots in = literature paper PDFs, under educational fair use?  Unfortunately, = Google did not seem to help me this time... = :-)

 

Thanks,

Andrew DeYoung

Carnegie Mellon University

andrewdaviddeyoung AT gmail.com

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