From owner-chemistry@ccl.net Sat Aug 19 01:26:00 2017 From: "Andrew Rosen rosen/a\u.northwestern.edu" To: CCL Subject: CCL:G: Base split valence in Gaussian Message-Id: <-52931-170819012448-29940-QDHOPfQqNbsLbmWP3h0Bvw]=[server.ccl.net> X-Original-From: Andrew Rosen Content-Type: multipart/alternative; boundary="001a113cd8786197bf05571476d3" Date: Sat, 19 Aug 2017 05:24:30 +0000 MIME-Version: 1.0 Sent to CCL by: Andrew Rosen [rosen\a/u.northwestern.edu] --001a113cd8786197bf05571476d3 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Leila, The SVP+SP basis set is not a default keyword in Gaussian. In this paper that you are referring to, they discuss how to construct the basis set, which you'd have to do yourself if you wish to reproduce their results. Note that this will likely require use of the `gen` keyword in Gaussian. Keep in mind that since this paper was published in 2002, if you wish to reproduce their results, you shouldn't use def2-SVP (although it is generally recommended to use the def2 family in practice). The Ahlrichs def2 family of basis sets did not come out until 2005/2006. Andrew > On Fri, Aug 18, 2017 at 12:56 PM Leila Carvalho < > leilacardoso.quim%x%gmail.com> wrote: > >> Hi! >> >> I am reproducing an article an basis set is SVP+sp and I'm not obtaining >> success. >> *(Article: Solvent Effects on Hydrogen Bonds- A Theoretical Study, of >> Ad=C3=A9lia Aquino*). >> >> Thanks, >> Leila. >> > On Thu, Aug 17, 2017 at 8:08 PM Leila Cardoso Carvalho leilacardoso.quim!^! gmail.com wrote: > > Sent to CCL by: "Leila Cardoso Carvalho" [leilacardoso.quim:gmail.com] > Dear! > > I'm working with Gaussian and I'm having difficulty with the input of the > base SVP + sp because it gives an error in the command. Can you suggest t= he > input command used to run the base SVP + sp in the Gaussian 03 to optimiz= e > the geometry of a molecule? > > Thankful, > Leila > leilacardoso.quim:_:gmail.com > Universidade Federal do Oeste da Bahia-UFOB > Rua Professor Jos Seabra de Lemos, 316. > Recanto dos Pssaros. > CEP: 47808-021 > Barreiras BA > > Fone: 77 3614-3196 > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a113cd8786197bf05571476d3 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Leila,=C2=A0
The SVP+SP basis set is not a default keyword in Gaussian. In=C2=A0this paper<= /a>=C2=A0that you are referring to, they discuss how to construct the basis= set, which you'd have to do yourself if you wish to reproduce their re= sults. Note that this will likely require use of the `gen`=C2=A0keyword=C2=A0in Gaussian.

Keep in mind that since this paper was published in 2002, if you w= ish to reproduce their results, you shouldn't use def2-SVP (although it= is generally recommended to use the def2 family in practice). The Ahlrichs= def2 family of basis sets did not come out until 2005/2006.

Andr= ew

On Fri, Aug 18, 2017 at 12:56 PM Leila Carvalho &= lt;leilaca= rdoso.quim%x%gmail.com> wrote:
<= div class=3D"gmail_quote">
Hi!

I am reproducing an article an bas= is set is SVP+sp and I'm not obtaining success.
(Article: Solvent Effects on Hydr= ogen Bonds- A Theoretical Study, of Ad=C3=A9lia Aquino).

Tha= nks,=C2=A0
Leila.

On Thu, Aug 17, 2017 at 8:08 PM Leila Cardoso Carvalho leilac= ardoso.quim!^!gmail.com <owner-chemistry%x%ccl.net> wrote:

Sent to CCL by: "Leila Cardoso Carvalho" [leilacardoso.quim:gmail.com]=
Dear!

I'm working with Gaussian and I'm having difficulty with the input = of the
base SVP + sp because it gives an error in the command. Can you suggest the=
input command used to run the base SVP + sp in the Gaussian 03 to optimize<= br> the geometry of a molecule?

Thankful,
Leila
leilacardoso.quim:_:gmail.com
Universidade Federal do Oeste da Bahia-UFOB
Rua Professor Jos Seabra de Lemos, 316.
Recanto dos Pssaros.
CEP: 47808-021
Barreiras=C2=A0 BA

Fone: 77 3614-3196



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VW5pcXVlSUR9IiBzdHlsZT0iRk9OVC1TSVpFOiA4cHQiPjwvcD4NCjwvYm9keT4NCjwvaHRtbD4N Cg== --_000_0D1AB13C4E3B4927BA0CF30F76D8951Eastrazenecacom_-- From owner-chemistry@ccl.net Sat Aug 19 15:19:01 2017 From: "Tibor Gyori tiborgyri]_[gmail.com" To: CCL Subject: CCL: Performance of AMD Ryzen CPUs ? Message-Id: <-52933-170819081501-11756-HykwbbQ+XhTiGWu2jrMXlw- -server.ccl.net> X-Original-From: "Tibor Gyori" Date: Sat, 19 Aug 2017 08:15:00 -0400 Sent to CCL by: "Tibor Gyori" [tiborgyri(-)gmail.com] Dear CCL Subscribers, Recently AMD has released a number of new CPUs, with greatly improved performance and power efficiency compared to their previous products, and they are priced very competitively. (only 300 USD for the cheapest 8-core CPU, 1000 USD for a 16 core CPU) The deal is further sweetened by the fact that all of these ordinary desktop parts support ECC memory.(unbuffered only, so 64/128 GB max.) While there is little relevant data available online, it seems clear that highly parallel tasks (with little or no communication between threads) run very well. (NAMD seems to perform particularly well on Ryzen) My question is that does anyone here have any experience regarding the performance of Ryzen/Threadripper/Epyc CPUs in computational chemistry workloads? Information on quantum chemistry performance (PSI4, Molpro, MRCC, Orca, etc.) would be especially useful for our research group. Thanks, Tibor Gyori MSc. student University of Szeged From owner-chemistry@ccl.net Sat Aug 19 15:54:01 2017 From: "Igors Mihailovs igorsm**cfi.lu.lv" To: CCL Subject: CCL:G: Vibrational sublevels along particular coordinate on PES Message-Id: <-52934-170819103840-17428-nvsGz15FNA/ho9APjf5sUw%a%server.ccl.net> X-Original-From: Igors Mihailovs Content-Language: en-US Content-Type: multipart/alternative; boundary="------------2FA02B23388C8B4816DA181D" Date: Sat, 19 Aug 2017 17:40:48 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm(~)cfi.lu.lv] This is a multi-part message in MIME format. --------------2FA02B23388C8B4816DA181D Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Dear Dr. Norrby, Thank You for Your reply! But it seems to me that I might have been right about that 'nonsence' in my question, because either I am misinterpreting Your answer or You may have misinterpreted my question. Or both :) So I will describe my actual situation then. I have a discussion with a synthetic chemist about interpreting the results of this PES scan. There are actually two different scans, one in benzene and another one in acetonitrile, with notably lower barrier in acetonitrile. One of his arguments is that in acetonitrile there is larger population of conformations with non-equilibrium dihedral values (then it might help to interpret some experimental findings about a certain molecular electronic property). If calculated according to Boltzmann distribution, some conformations with moderate deviations from the equilibrium value of dihedral do have significant population with respect to the equilibrium one (e.g., 0.2:1), because PES is relatively flat in that region. If I do understand correctly, in reality only those conformations are really present in solution which correspond to some vibrational sublevels on PES (or should it be free-energy surface then?). I thought I could determine if a conformation is something real if I plot vibrational sublevels in the well and check whether a conformation is higher or lower than the first of sublevels,… and so on. Is this the right idea at all? If it is, should these sublevels be taken > from the calculations of stationary points (well bottoms), or should I project those sublevels, or …? Because I cannot even found meaning of those 'projected contributions' in my interpretation of how PES is related to vibrational sublevels (above). So is this interpretation rather wrong?… Thank You (and possibly others) again in advance. Yours sincerely, Igors Mihailovs PhD student ISSP University of Latvia On 19/08/17 10:19, Norrby, Per-Ola Per-Ola.Norrby]|[astrazeneca.com wrote: > Dear Igors, > > Adding vibrational contributions makes most sense at stationary > points, you can use them when comparing stationary points, like the > (fully converged) minima and transition state. If you need to, there > is a way to calculate these contributions also at non-stationary > points using Freq=Project in Gaussian. Note that you lose one degree > of freedom, the direction of the force, which is projected out > together with the translations and rotations (giving you N-7 degrees > of freedom, not the usual N-6). > > Per-Ola > > Sent from my iPhone > > On 18 Aug 2017, at 19:06, Igors Mihailovs igorsm=-=cfi.lu.lv > > wrote: > >> Dear computational chemistry specialists, >> >> I have a question possibly of general knowledge (which I lack), >> considering transfer of what I have learned about levels and >> sublevels of diatomics to calculations of "big" molecules. >> I am trying to analyze the potential energy surface of a particular >> compound along one particular dihedral (by doing partial >> optimizations at various values of this dihedral). This cut of PES >> has double concave shape (like the small Greek lambda), as if there >> were two potential wells separated by a barrier (ca. 15 kcal/mol), >> corresponding to two conformers. If I would be supposed to draw >> vibrational sublevels in both wells, what would be their energies? >> The computed vibrational frequencies (for stable structures at >> bottoms of both wells) with respect to some line over the bottom? >> The bottom should be the zero-point vibrational energy, but then the >> one computed by Gaussian is about 70 times larger than the barrier >> between two conformers (ca. 1015 kcal/mol). I suppose I should take >> only contribution to ZPE from the dihedral in interest to determine >> the first level in a well (since all the modes are complex, do I need >> some diagonalization of something, like to get "natural frequency >> modes"?). Is this so? If not, does this result mean there is constant >> interconversion of both conformers (sounds a bit ridiculous to me)? >> Or is this whole idea of drawing vibration levels over such a cut in >> PES just a nonsence? >> >> Sorry for my illiteracy. And thanks in advance! >> >> With best regards, >> Igors Mihailovs >> PhD student >> ISSP University of Latvia > ------------------------------------------------------------------------ > > *Confidentiality Notice: *This message is private and may contain > confidential and proprietary information. If you have received this > message in error, please notify us and remove it from your system and > note that you must not copy, distribute or take any action in reliance > on it. Any unauthorized use or disclosure of the contents of this > message is not permitted and may be unlawful. > --------------2FA02B23388C8B4816DA181D Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Dear Dr. Norrby,

Thank You for Your reply! But it seems to me that I might have been right about that 'nonsence' in my question, because either I am misinterpreting Your answer or You may have misinterpreted my question. Or both :)

So I will describe my actual situation then. I have a discussion with a synthetic chemist about interpreting the results of this PES scan. There are actually two different scans, one in benzene and another one in acetonitrile, with notably lower barrier in acetonitrile. One of his arguments is that in acetonitrile there is larger population of conformations with non-equilibrium dihedral values (then it might help to interpret some experimental findings about a certain molecular electronic property). If calculated according to Boltzmann distribution, some conformations with moderate deviations from the equilibrium value of dihedral do have significant population with respect to the equilibrium one (e.g., 0.2:1), because PES is relatively flat in that region. If I do understand correctly, in reality only those conformations are really present in solution which correspond to some vibrational sublevels on PES (or should it be free-energy surface then?). I thought I could determine if a conformation is something real if I plot vibrational sublevels in the well and check whether a conformation is higher or lower than the first of sublevels,… and so on. Is this the right idea at all? If it is, should these sublevels be taken from the calculations of stationary points (well bottoms), or should I project those sublevels, or …? Because I cannot even found meaning of those 'projected contributions' in my interpretation of how PES is related to vibrational sublevels (above). So is this interpretation rather wrong?…

Thank You (and possibly others) again in advance.

Yours sincerely,
Igors Mihailovs
PhD student
ISSP University of Latvia


On 19/08/17 10:19, Norrby, Per-Ola Per-Ola.Norrby]|[astrazeneca.com wrote:
Dear Igors,

Adding vibrational contributions makes most sense at stationary points, you can use them when comparing stationary points, like the (fully converged) minima and transition state. If you need to, there is a way to calculate these contributions also at non-stationary points using Freq=Project in Gaussian. Note that you lose one degree of freedom, the direction of the force, which is projected out together with the translations and rotations (giving you N-7 degrees of freedom, not the usual N-6).

Per-Ola

Sent from my iPhone

On 18 Aug 2017, at 19:06, Igors Mihailovs igorsm=-=cfi.lu.lv <owner-chemistry^ccl.net> wrote:

Dear computational chemistry specialists,

I have a question possibly of general knowledge (which I lack), considering transfer of what I have learned about levels and sublevels of diatomics to calculations of "big" molecules.
I am trying to analyze the potential energy surface of a particular compound along one particular dihedral (by doing partial optimizations at various values of this dihedral). This cut of PES has double concave shape (like the small Greek lambda), as if there were two potential wells separated by a barrier (ca. 15 kcal/mol), corresponding to two conformers. If I would be supposed to draw vibrational sublevels in both wells, what would be their energies? The computed vibrational frequencies (for stable structures at bottoms of both wells) with respect to some line over the bottom?
The bottom should be the zero-point vibrational energy, but then the one computed by Gaussian is about 70 times larger than the barrier between two conformers (ca. 1015 kcal/mol). I suppose I should take only contribution to ZPE from the dihedral in interest to determine the first level in a well (since all the modes are complex, do I need some diagonalization of something, like to get "natural frequency modes"?). Is this so? If not, does this result mean there is constant interconversion of both conformers (sounds a bit ridiculous to me)? Or is this whole idea of drawing vibration levels over such a cut in PES just a nonsence?

Sorry for my illiteracy. And thanks in advance!

With best regards,
Igors Mihailovs
PhD student
ISSP University of Latvia

Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.


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