From owner-chemistry@ccl.net Fri May 7 12:26:00 2021 From: "Andrew DeYoung andrewdaviddeyoung|*|gmail.com" To: CCL Subject: CCL: How to find data files for experimentally-obtained RDFs of water Message-Id: <-54323-210507121749-24674-rJ6uWjhxiWd+5G17dcRIog{:}server.ccl.net> X-Original-From: Andrew DeYoung Content-Type: multipart/alternative; boundary="00000000000010459d05c1bfc403" Date: Fri, 7 May 2021 12:17:29 -0400 MIME-Version: 1.0 Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung a gmail.com] --00000000000010459d05c1bfc403 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi all, Thank you so much for your help finding data files for experimentally-obtained RDFs for water! You are so generous with your time= ! Thank you, Andrew DeYoung Carnegie Mellon University On Mon, May 3, 2021 at 9:12 PM Carlos Simmerling carlos.simmerling(a) gmail.com wrote: > 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 Func= tion 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.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 a= m >> 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 s= ee >> 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 th= e >> 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 >> > --00000000000010459d05c1bfc403 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all,

Thank you so much fo= r your help finding data files for experimentally-obtained RDFs for water!= =C2=A0 You are so generous with your time!

Thank y= ou,
Andrew DeYoung
Carnegie Mellon University

=
On Mon, Ma= y 3, 2021 at 9:12 PM Carlos Simmerling carlos.simmerling(a)gmail.com <o= wner-chemistry _ ccl.net> wrote:
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=A0Pettersson, L. G. M.;=C2=A0Nilsson, A.;=C2=A0Benmore, C. J.=C2=A0Benchmark Oxygen=E2=80=93Oxygen Pair-Dis= tribution Function of Ambient Water from X-Ray Diffraction Measurements wit= h a Wide Q-Range=C2=A0J. Chem. Phys.=C2=A02013,=C2=A0138,=C2=A0<= /span>074506

On Mon, May 3, 2021 at 6:00 PM Andrew DeYoung andrewdaviddeyou= ng[*]gmail.com <owner-chemistry]_= [ccl.net> wrote:
Hi,

I am mentoring a= first-year undergraduate in computational chemistry.=C2=A0 I am having him= run a brief MD simulation of water at 300 K and calculate the radial distr= ibution functions (RDFs) g_OO(r), g_OH(r), and g_HH(r).=C2=A0 I am not an e= xperimentalist, 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
--00000000000010459d05c1bfc403-- From owner-chemistry@ccl.net Fri May 7 13:00:00 2021 From: "Andrew DeYoung andrewdaviddeyoung ~ gmail.com" To: CCL Subject: CCL:G: A mailing list, forum, or Q&A site for Gaussian Message-Id: <-54324-210507122450-25265-gbiO0QEWfaR9kb5q2qDYKw]|[server.ccl.net> X-Original-From: Andrew DeYoung Content-Type: multipart/alternative; boundary="0000000000004b9ce905c1bfdd49" Date: Fri, 7 May 2021 12:24:33 -0400 MIME-Version: 1.0 Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung|,|gmail.com] --0000000000004b9ce905c1bfdd49 Content-Type: text/plain; charset="UTF-8" Hi, Can anyone recommend a mailing list, forum, or Q&A site for questions about Gaussian 16? (Other than asking questions directly to Gaussian tech support or on here, CCL. Everyone here on CCL seems generous with their time, but I don't want to bother you all with boring technical questions about Gaussian.) A lot of other packages (e.g., GROMACS, NAMD, VMD) have dedicated forums or mailing lists, but offhand I don't see any for Gaussian. Thank you, Andrew DeYoung Carnegie Mellon University --0000000000004b9ce905c1bfdd49 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

Can anyone recommend=C2=A0a mailing= list, forum, or Q&A site for questions about Gaussian 16?=C2=A0 (Other= than asking questions directly to Gaussian tech support or on here, CCL.= =C2=A0 Everyone here on CCL seems generous with their time, but I don't= want to bother you all with boring technical questions about Gaussian.)=C2= =A0 A lot of other packages (e.g., GROMACS, NAMD, VMD) have dedicated forum= s or mailing lists, but offhand I don't see any for Gaussian.

Thank you,
Andrew DeYoung
Carnegie Mell= on University
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