From owner-chemistry@ccl.net Tue May 4 06:20:01 2021
From: "Andrey KALINICHEV kalinich : subatech.in2p3.fr" <owner-chemistry[]server.ccl.net>
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 <kalinich:-:subatech.in2p3.fr>
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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 <http://gmail.com>
From owner-chemistry@ccl.net Tue May 4 06:54:01 2021
From: "Jacek Korchowiec korchow^-^chemia.uj.edu.pl" <owner-chemistry-x-server.ccl.net>
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" <korchow(!)chemia.uj.edu.pl>
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" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL: How to find data files for experimentally-obtained RDFs of water
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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 =
<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
=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 <http://gmail.com>=20
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class=3DWordSection1><p class=3DMsoNormal><span =
style=3D'font-size:12.0pt;font-family:"Palatino Linotype",serif'>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.<o:p></o:p></span></p><p class=3DMsoNormal><span =
style=3D'font-size:12.0pt;font-family:"Palatino =
Linotype",serif'><o:p> </o:p></span></p><p class=3DMsoNormal><span =
style=3D'font-size:12.0pt;font-family:"Palatino =
Linotype",serif'>Dominic<o:p></o:p></span></p><p class=3DMsoNormal><span =
style=3D'font-size:12.0pt;font-family:"Palatino =
Linotype",serif'><o:p> </o:p></span></p><div =
style=3D'border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in =
0in 0in'><p class=3DMsoNormal><b>From:</b> =
owner-chemistry+m.dominic.ryan=3D=3Dgmail.com^-^ccl.net =
<owner-chemistry+m.dominic.ryan=3D=3Dgmail.com^-^ccl.net> <b>On =
Behalf Of </b>Andrew DeYoung =
andrewdaviddeyoung[*]gmail.com<br><b>Sent:</b> Monday, May 3, 2021 3:45 =
PM<br><b>To:</b> Ryan, M Dominic =
<m.dominic.ryan^-^gmail.com><br><b>Subject:</b> CCL: How to find =
data files for experimentally-obtained RDFs of =
water<o:p></o:p></p></div><p =
class=3DMsoNormal><o:p> </o:p></p><div><div><p =
class=3DMsoNormal>Hi,<o:p></o:p></p></div><div><p =
class=3DMsoNormal><o:p> </o:p></p></div><div><p class=3DMsoNormal>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. =
<o:p></o:p></p></div><div><p =
class=3DMsoNormal><o:p> </o:p></p></div><div><p class=3DMsoNormal>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.<o:p></o:p></p></div><div><p =
class=3DMsoNormal><o:p> </o:p></p></div><div><p =
class=3DMsoNormal>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... =
:-)<o:p></o:p></p></div><div><p =
class=3DMsoNormal><o:p> </o:p></p></div><div><p =
class=3DMsoNormal>Thanks,<o:p></o:p></p></div><div><p =
class=3DMsoNormal>Andrew DeYoung<o:p></o:p></p></div><div><p =
class=3DMsoNormal>Carnegie Mellon University<o:p></o:p></p></div><div><p =
class=3DMsoNormal>andrewdaviddeyoung AT <a =
href=3D"http://gmail.com">gmail.com</a><o:p></o:p></p></div></div></div><=
/body></html>
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