From owner-chemistry@ccl.net Mon May 3 04:27:00 2021 From: "Roland Stote rstote===unistra.fr" To: CCL Subject: CCL: Online meeting of the ISQBP 2021, June 29 to July 1 Message-Id: <-54315-210503042056-30646-9piA3eCI0t1rOUh4oJYgfw-,-server.ccl.net> X-Original-From: "Roland Stote" Date: Mon, 3 May 2021 04:20:55 -0400 Sent to CCL by: "Roland Stote" [rstote{}unistra.fr] Dear Colleagues, We are happy to announce the 2021 Online Meeting of the International Society of Quantum Biology and Pharmacology (ISQBP). For the past 51 years, the ISQBP has organized dynamic biennial meetings providing a forum to discuss and extend the impact of computational methodologies in the fields of biology, chemistry, chemical biology, and pharmacology. We will host the 2021 meeting online from June 29th to July 1st 2021. Registration is now open; the website for the meeting with the list of confirmed speakers is available at the webpage: https://isqbp2021.sciencesconf.org Early-Bird registration deadline is May 6, 2021. Abstract submission deadline is May 15, 2021. We are looking forward to having you join us for this exciting meeting being organized from Strasbourg, France. Best regards, The Scientific Organizing Committee, Annick Dejaegere, Nathalie Reuter and Roland Stote From owner-chemistry@ccl.net Mon May 3 15:56:01 2021 From: "Andrew DeYoung andrewdaviddeyoung[*]gmail.com" To: CCL Subject: CCL: How to find data files for experimentally-obtained RDFs of water Message-Id: <-54316-210503154510-4874-++ctdIueFEI+z2PbeL++PQ(_)server.ccl.net> X-Original-From: Andrew DeYoung Content-Type: multipart/alternative; boundary="0000000000000fe20e05c17232a8" Date: Mon, 3 May 2021 15:44:42 -0400 MIME-Version: 1.0 Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung|gmail.com] --0000000000000fe20e05c17232a8 Content-Type: text/plain; charset="UTF-8" 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 --0000000000000fe20e05c17232a8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

I am mentoring a first-y= ear undergraduate in computational chemistry.=C2=A0 I am having him run a b= rief MD simulation of water at 300 K and calculate the radial distribution = functions (RDFs) g_OO(r), g_OH(r), and g_HH(r).=C2=A0 I am not an experimen= talist, but I understand that those RDFs can be obtained from some clever m= easurements, such as X-ray scattering.=C2=A0

= I would like to have my=20 undergraduate=20 student overlay his RDFs (obtained from simulation) on top of experimentall= y-obtained RDFs so that he can see that even a relatively simple water mode= l such as SPC does a reasonable job of reproducing the experimental structu= res.=C2=A0 In the literature there are lots of papers that make such compar= isons between simulation and experiment, but if possible, I would like my s= tudent to actually plot the comparisons himself.

D= oes anyone have any idea where I can find data files for experimentally-obt= ained RDFs (i.e., just=20 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?=C2=A0 Unf= ortunately, Google did not seem to help me this time... :-)

<= /div>
Thanks,
Andrew DeYoung
Carnegie Mellon Univer= sity
andrewdaviddeyoung AT gmail.com
--0000000000000fe20e05c17232a8-- From owner-chemistry@ccl.net Mon May 3 17:28:00 2021 From: "Andre Farias de Moura moura%%ufscar.br" To: CCL Subject: CCL: How to find data files for experimentally-obtained RDFs of water Message-Id: <-54317-210503172652-21170-7gsl+7ELviP1JqltgjM1Cw- -server.ccl.net> X-Original-From: Andre Farias de Moura Content-Type: multipart/alternative; boundary="00000000000013600c05c1739e71" Date: Mon, 3 May 2021 18:26:30 -0300 MIME-Version: 1.0 Sent to CCL by: Andre Farias de Moura [moura~!~ufscar.br] --00000000000013600c05c1739e71 Content-Type: text/plain; charset="UTF-8" Dear Andrew, I suggest you get in touch with Dr. Felippe Colombari ( colombarifm%a%hotmail.com), he did some nice theoretical-experimental collaboration recently, using pair distribution functions obtained for water from Cryo-TEM experiments. Regards Andre On Mon, May 3, 2021 at 6:06 PM Andrew DeYoung andrewdaviddeyoung[*]gmail.com wrote: > 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 > --00000000000013600c05c1739e71 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Andrew,

I suggest you g= et in touch with Dr. Felippe Colombari (colombarifm%a%hotmail.com), he did some nice theoretical-experime= ntal collaboration recently, using pair distribution functions obtained for= water from Cryo-TEM experiments.

Regards

Andre

On Mon, May 3, 2021 at 6:06 PM Andrew DeYou= ng andrewdaviddeyoung[*]gmail.com <owner-chemistry%a%ccl.net> wrot= e:
Hi,

I am mentoring a first-year undergrad= uate in computational chemistry.=C2=A0 I am having him run a brief MD simul= ation of water at 300 K and calculate the radial distribution functions (RD= Fs) g_OO(r), g_OH(r), and g_HH(r).=C2=A0 I am not an experimentalist, but I= understand that those RDFs can be obtained from some clever measurements, = such as X-ray scattering.=C2=A0

I would like = to have my=20 undergraduate=20 student overlay his RDFs (obtained from simulation) on top of experimentall= y-obtained RDFs so that he can see that even a relatively simple water mode= l such as SPC does a reasonable job of reproducing the experimental structu= res.=C2=A0 In the literature there are lots of papers that make such compar= isons between simulation and experiment, but if possible, I would like my s= tudent to actually plot the comparisons himself.

D= oes anyone have any idea where I can find data files for experimentally-obt= ained RDFs (i.e., just=20 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?=C2=A0 Unf= ortunately, Google did not seem to help me this time... :-)

<= /div>
Thanks,
Andrew DeYoung
Carnegie Mellon Univer= sity
andrewdaviddeyoung AT gmail.= com
--00000000000013600c05c1739e71-- From owner-chemistry@ccl.net Mon May 3 19:01:01 2021 From: "Carlos Simmerling carlos.simmerling(a)gmail.com" To: CCL Subject: CCL: How to find data files for experimentally-obtained RDFs of water Message-Id: <-54318-210503185539-28326-1OJ8AHXBIOjY3PD3wpkX6Q=-=server.ccl.net> X-Original-From: Carlos Simmerling Content-Type: multipart/alternative; boundary="00000000000094638805c174dbc4" Date: Mon, 3 May 2021 18:55:02 -0400 MIME-Version: 1.0 Sent to CCL by: Carlos Simmerling [carlos.simmerling:_:gmail.com] --00000000000094638805c174dbc4 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable you can try this for O-O (I don't have any references for data involving H)= : Skinner, L. B.; Huang, C.; Schlesinger, D.; Pettersson, L. G. M.; Nilsson, A.; Benmore, C. J. Benchmark Oxygen=E2=80=93Oxygen Pair-Distribution Functi= on of Ambient Water from X-Ray Diffraction Measurements with a Wide Q-Range J. Chem. Phys. 2013, 138, 074506 On Mon, May 3, 2021 at 6:00 PM Andrew DeYoung andrewdaviddeyoung[*]gmail.co= m wrote: > 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 t= he > 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 se= e > that even a relatively simple water model such as SPC does a reasonable j= ob > 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)) f= or > 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 > --00000000000094638805c174dbc4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
you can try this for O-O (I don't have any references = for data involving H):
Skinner, L. B.;= =C2=A0Huang, C.;=C2=A0Schlesinger, D.;=C2=A0Pette= rsson, L. G. M.;=C2=A0Nilsson, A.;=C2=A0Benmore, C. J.=C2=A0Benchmark O= xygen=E2=80=93Oxygen Pair-Distribution Function of Ambient Water from X-Ray= Diffraction Measurements with a Wide Q-Range=C2=A0<= span class=3D"gmail-citation_source-journal" style=3D"box-sizing:border-box= ;outline:none;display:inline;color:rgb(0,0,0);font-family:Roboto,arial,sans= -serif;font-size:13px">J. Chem. Phys.=C2=A02013,=C2=A0= 138,=C2=A0074506

On Mon, May 3, 2021 at 6:00 PM Andrew DeYoung andrewdaviddeyoung[*]gmail.com <owner-chemistry(a)ccl.net> wrote:
Hi,

<= /div>
I am mentoring a first-year undergraduate in computational chemis= try.=C2=A0 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).=C2=A0 I am not an experimentalist, but I understand that those RDFs = can be obtained from some clever measurements, such as X-ray scattering.=C2= =A0

I would like to have my=20 undergraduate=20 student overlay his RDFs (obtained from simulation) on top of experimentall= y-obtained RDFs so that he can see that even a relatively simple water mode= l such as SPC does a reasonable job of reproducing the experimental structu= res.=C2=A0 In the literature there are lots of papers that make such compar= isons between simulation and experiment, but if possible, I would like my s= tudent to actually plot the comparisons himself.

D= oes anyone have any idea where I can find data files for experimentally-obt= ained RDFs (i.e., just=20 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?=C2=A0 Unf= ortunately, Google did not seem to help me this time... :-)

<= /div>
Thanks,
Andrew DeYoung
Carnegie Mellon Univer= sity
andrewdaviddeyoung AT gmail.= com
--00000000000094638805c174dbc4--