From owner-chemistry@ccl.net Sat Jul 9 08:57:00 2022 From: "Grigoriy Zhurko reg_zhurko.:.chemcraftprog.com" To: CCL Subject: CCL: Negative frequencies with C1 symmetry (Orca) Message-Id: <-54747-220709083113-26708-ubFlmzemPEfkW4TqRRLONw::server.ccl.net> X-Original-From: "Grigoriy Zhurko" Date: Sat, 9 Jul 2022 08:31:08 -0400 Sent to CCL by: "Grigoriy Zhurko" [reg_zhurko()chemcraftprog.com] Hello, I compute some molecules with Orca 5.0.3, and the computation sometimes produces small negative frequencies, despite the symmetry of the molecules is C1. If I repeat the computation with another starting point, with some probability all frequencies are positive. I found that this problem arises when two additions to the model are added: the solvent model (!CPCM(Water)) and additions of some explicit water molecules to the whole model. I understand that these water molecules produce very small frequencies along the h-bonds, and these frequencies can become negative because of some problems with numerical integration. I tried the combination of options !DefGrid3, !TightOpt, !VeryTightSCF, and still sometimes the negative frequencies are produced. Maybe I need to further increase the computational accuracy with options like "!VeryTightOpt", "!DefGrid9", UltraTightSCF? I suppose you understand what I mean; currently I didn't find the information in the manual, how to further decrease the optimization convergence threshold or increase the accuracy of DFT grid. Please suggest how to do that. In my work I can avoid using the frequencies since I need mainly the energies; however I need to explain this somehow in the paper. I suppose, it is not good to compute the entropy of molecules with my keywords, because small frequencies produce big errors with vibrational entropy. So, please suggest me, what should I write in my papers, to explain that it is not good to compute the Gibbs energy of my molecules, but it is correct to compute and use the common energy. Grigoriy Zhurko https://chemcraftprog.com From owner-chemistry@ccl.net Sat Jul 9 13:38:00 2022 From: "Anatoli Korkin korkin_-_nanoandgiga.com" To: CCL Subject: CCL: Negative frequencies with C1 symmetry (Orca) Message-Id: <-54748-220709133226-32518-cAxdac+z2cmC44+ppphDfg]![server.ccl.net> X-Original-From: Anatoli Korkin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Sat, 9 Jul 2022 10:32:19 -0700 Mime-Version: 1.0 (1.0) Sent to CCL by: Anatoli Korkin [korkin##nanoandgiga.com] You should not write a scientific paper without basic understanding of what you are doing! Sent from my iPhone > On Jul 9, 2022, at 6:52 AM, Grigoriy Zhurko reg_zhurko.:.chemcraftprog.com wrote: > >  > Sent to CCL by: "Grigoriy Zhurko" [reg_zhurko()chemcraftprog.com] > Hello, > I compute some molecules with Orca 5.0.3, and the computation sometimes > produces small negative frequencies, despite the symmetry of the molecules is > C1. If I repeat the computation with another starting point, with some > probability all frequencies are positive. > I found that this problem arises when two additions to the model are added: > the solvent model (!CPCM(Water)) and additions of some explicit water > molecules to the whole model. I understand that these water molecules produce > very small frequencies along the h-bonds, and these frequencies can become > negative because of some problems with numerical integration. I tried the > combination of options !DefGrid3, !TightOpt, !VeryTightSCF, and still > sometimes the negative frequencies are produced. Maybe I need to further > increase the computational accuracy with options like "!VeryTightOpt", > "!DefGrid9", UltraTightSCF? I suppose you understand what I mean; currently > I didn't find the information in the manual, how to further decrease the > optimization convergence threshold or increase the accuracy of DFT grid. > Please suggest how to do that. > In my work I can avoid using the frequencies since I need mainly the > energies; however I need to explain this somehow in the paper. I suppose, it > is not good to compute the entropy of molecules with my keywords, because > small frequencies produce big errors with vibrational entropy. So, please > suggest me, what should I write in my papers, to explain that it is not good > to compute the Gibbs energy of my molecules, but it is correct to compute and > use the common energy. > > Grigoriy Zhurko > https://chemcraftprog.com> > From owner-chemistry@ccl.net Sat Jul 9 17:46:00 2022 From: "Soren Eustis soreneustis|-|gmail.com" To: CCL Subject: CCL: Negative frequencies with C1 symmetry (Orca) Message-Id: <-54749-220709173255-27656-u0X/E1NtS7r8YQSI0tOA4Q/a\server.ccl.net> X-Original-From: Soren Eustis Content-Type: multipart/alternative; boundary="62c9f3ff_2ca88611_2912" Date: Sat, 9 Jul 2022 17:32:28 -0400 MIME-Version: 1.0 Sent to CCL by: Soren Eustis [soreneustis()gmail.com] --62c9f3ff_2ca88611_2912 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hey, be respectful and open to questions from newcomers or established sc= ientists.=C2=A0=C2=A0I understood exactly what Grigoriy was talking about= . In this case Grigoriy, happens to have made massive contributions to ou= r community- including coding ChemCraft. If I were to try to discuss the complexities of the field in any other la= nguage than my native tongue, I=E2=80=99d be at a loss. Primarily, let=E2=80=99s be better to people here. In this case, Grigoriy= is a world class scientist who deserves respect. Most importantly, even = the brightest minds need to start somewhere. I spent a lot of time trying= to have questions answered here as a new scientist and some people were = pretty harsh. Some weren=E2=80=99t. Now I have published many papers and = trained many scientists in the field. Be kind. Soren On Jul 9, 2022, 15:01 -0400, Anatoli Korkin korkin=5F-=5Fnanoandgiga.com = , wrote: > > Sent to CCL by: Anatoli Korkin =5Bkorkin=23=23nanoandgiga.com=5D > You should not write a scientific paper without basic understanding of = what you are doing=21 > > Sent from my iPhone > > > On Jul 9, 2022, at 6:52 AM, Grigoriy Zhurko reg=5Fzhurko.:.chemcraftp= rog.com wrote: > > > > > > Sent to CCL by: =22Grigoriy Zhurko=22 =5Breg=5Fzhurko()chemcraftprog.= com=5D > > Hello, > > I compute some molecules with Orca 5.0.3, and the computation sometim= es > > produces small negative frequencies, despite the symmetry of the mole= cules is > > C1. If I repeat the computation with another starting point, with som= e > > probability all frequencies are positive. > > I found that this problem arises when two additions to the model are = added: > > the solvent model (=21CPCM(Water)) and additions of some explicit wat= er > > molecules to the whole model. I understand that these water molecules= produce > > very small frequencies along the h-bonds, and these frequencies can b= ecome > > negative because of some problems with numerical integration. I tried= the > > combination of options =21DefGrid3, =21TightOpt, =21VeryTightSC=46, a= nd still > > sometimes the negative frequencies are produced. Maybe I need to furt= her > > increase the computational accuracy with options like =22=21VeryTight= Opt=22, > > =22=21DefGrid9=22, UltraTightSC=46=3F I suppose you understand what I= mean; currently > > I didn't find the information in the manual, how to further decrease = the > > optimization convergence threshold or increase the accuracy of D=46T = grid. > > Please suggest how to do that. > > In my work I can avoid using the frequencies since I need mainly the > > energies; however I need to explain this somehow in the paper. I supp= ose, it > > is not good to compute the entropy of molecules with my keywords, bec= ause > > small frequencies produce big errors with vibrational entropy. So, pl= ease > > suggest me, what should I write in my papers, to explain that it is n= ot good > > to compute the Gibbs energy of my molecules, but it is correct to com= pute and > > use the common energy. > > > > Grigoriy Zhurko > > https://chemcraftprog.com> > > > > > > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please chang= e > the strange characters on the top line to the =40 sign. You can also > look up the X-Original-=46rom: line in the mail header. > > E-mail to subscribers: CHEMISTRY=40ccl.net or use: > http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage > > E-mail to administrators: CHEMISTRY-REQUEST=40ccl.net or use > http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage> http://www.ccl.net/chemistry/sub=5Funsub.shtml=> > RT=46I: http://www.ccl.net/chemistry/aboutccl/instructions/ > > --62c9f3ff_2ca88611_2912 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hey, be respectful and open to questions from newco= mers or established scientists.&=23160;&=23160;I understood exactly what = Grigoriy was talking about. In this case Grigoriy, happens to have made m= assive contributions to our community- including coding ChemCraft.&=23160= ;&=23160;

If I were to try to discuss the complexities of the field in any other la= nguage than my native tongue, I=E2=80=99d be at a loss.

Primarily, let=E2=80=99s be better to people here. In this case, Grigoriy= is a world class scientist who deserves respect. Most importantly, even = the brightest minds need to start somewhere. I spent a lot of time trying= to have questions answered here as a new scientist and some people were = pretty harsh. Some weren=E2=80=99t. Now I have published many papers and = trained many scientists in the field. Be kind.

Soren&=23160;
On Jul 9, 2022, 15:01 -0400, Anatol= i Korkin korkin=5F-=5Fnanoandgiga.com <owner-chemistry=40ccl.net>, = wrote:

Sent to CCL by: Anatoli Korkin =5Bkorkin=23=23nanoandgiga.com=5D
You should not write a scientific paper without basic understanding of wh= at you are doing=21

Sent from my iPhone

On Jul 9, 2022, at 6:52 AM, Grigoriy Zhurko= reg=5Fzhurko.:.chemcraftprog.com <owner-chemistry*=5F*ccl.net> wro= te:

=EF=BB=BF
Sent to CCL by: =22Grigoriy Zhurko=22 =5Breg=5Fzhurko()chemcraftprog.com=5D=
Hello,
I compute some molecules with Orca 5.0.3, and the computation sometimes produces small negative frequencies, despite the symmetry of the molecule= s is
C1. If I repeat the computation with another starting point, with some probability all frequencies are positive.
I found that this problem arises when two additions to the model are adde= d:
the solvent model (=21CPCM(Water)) and additions of some explicit water molecules to the whole model. I understand that these water molecules pro= duce
very small frequencies along the h-bonds, and these frequencies can becom= e
negative because of some problems with numerical integration. I tried the=
combination of options =21DefGrid3, =21TightOpt, =21VeryTightSC=46, and s= till
sometimes the negative frequencies are produced. Maybe I need to further<= br /> increase the computational accuracy with options like =22=21VeryTightOpt=22= ,
=22=21DefGrid9=22, UltraTightSC=46=3F I suppose you understand what I mea= n; currently
I didn't find the information in the manual, how to further decrease the<= br /> optimization convergence threshold or increase the accuracy of D=46T grid= .
Please suggest how to do that.
In my work I can avoid using the frequencies since I need mainly the
energies; however I need to explain this somehow in the paper. I suppose,= it
is not good to compute the entropy of molecules with my keywords, because=
small frequencies produce big errors with vibrational entropy. So, please=
suggest me, what should I write in my papers, to explain that it is not g= ood
to compute the Gibbs energy of my molecules, but it is correct to compute= and
use the common energy.

Grigoriy Zhurko
https://chemcraftprog.com>




-=3D This is automatically added to each message by the mailing script =3D= -
the strange characters on the top line to the =40 sign. You can also
look up the X-Original-=46rom: line in the mail header.

E-mail to subscribers: CHEMISTRY=40ccl.net or use:
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--62c9f3ff_2ca88611_2912-- From owner-chemistry@ccl.net Sat Jul 9 20:19:01 2022 From: "Steve Williams willsd*appstate.edu" To: CCL Subject: CCL: [External] CCL: Negative frequencies with C1 symmetry (Orca) Message-Id: <-54750-220709200314-12099-XV5wdXsDCkIDZ8cul3EJaQ]_[server.ccl.net> X-Original-From: Steve Williams Content-Type: multipart/alternative; boundary="000000000000ee38a305e3682817" Date: Sat, 9 Jul 2022 20:02:54 -0400 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd[-]appstate.edu] --000000000000ee38a305e3682817 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Thank you Soren, for reminding me why Gregoriy has a familiar name .... I have been retired for a few years and no longer do computational chemistry anymore. But I used chemcraft for many years and convinced collaborators who were not computational chemists to buy copies also, so we could communicate well. So, yes, it is never wrong to be polite and helpful, and it is never wrong to NOT respond if polite and helpful is not your thing at the moment. Steve Williams On Sat, Jul 9, 2022, 6:49 PM Soren Eustis soreneustis|-|gmail.com < owner-chemistry(0)ccl.net> wrote: > Hey, be respectful and open to questions from newcomers or established > scientists. I understood exactly what Grigoriy was talking about. In thi= s > case Grigoriy, happens to have made massive contributions to our communit= y- > including coding ChemCraft. > > If I were to try to discuss the complexities of the field in any other > language than my native tongue, I=E2=80=99d be at a loss. > > Primarily, let=E2=80=99s be better to people here. In this case, Grigoriy= is a > world class scientist who deserves respect. Most importantly, even the > brightest minds need to start somewhere. I spent a lot of time trying to > have questions answered here as a new scientist and some people were pret= ty > harsh. Some weren=E2=80=99t. Now I have published many papers and trained= many > scientists in the field. Be kind. > > Soren > On Jul 9, 2022, 15:01 -0400, Anatoli Korkin korkin_-_nanoandgiga.com < > owner-chemistry(0)ccl.net>, wrote: > > > Sent to CCL by: Anatoli Korkin [korkin##nanoandgiga.com] > You should not write a scientific paper without basic understanding of > what you are doing! > > Sent from my iPhone > > On Jul 9, 2022, at 6:52 AM, Grigoriy Zhurko reg_zhurko.:.chemcraftprog.co= m > wrote: > > =EF=BB=BF > Sent to CCL by: "Grigoriy Zhurko" [reg_zhurko()chemcraftprog.com] > Hello, > I compute some molecules with Orca 5.0.3, and the computation sometimes > produces small negative frequencies, despite the symmetry of the molecule= s > is > C1. If I repeat the computation with another starting point, with some > probability all frequencies are positive. > I found that this problem arises when two additions to the model are adde= d: > the solvent model (!CPCM(Water)) and additions of some explicit water > molecules to the whole model. I understand that these water molecules > produce > very small frequencies along the h-bonds, and these frequencies can becom= e > negative because of some problems with numerical integration. I tried the > combination of options !DefGrid3, !TightOpt, !VeryTightSCF, and still > sometimes the negative frequencies are produced. Maybe I need to further > increase the computational accuracy with options like "!VeryTightOpt", > "!DefGrid9", UltraTightSCF? I suppose you understand what I mean; current= ly > I didn't find the information in the manual, how to further decrease the > optimization convergence threshold or increase the accuracy of DFT grid. > Please suggest how to do that. > In my work I can avoid using the frequencies since I need mainly the > energies; however I need to explain this somehow in the paper. I suppose, > it > is not good to compute the entropy of molecules with my keywords, because > small frequencies produce big errors with vibrational entropy. So, please > suggest me, what should I write in my papers, to explain that it is not > good > to compute the Gibbs energy of my molecules, but it is correct to compute > and > use the common energy. > > Grigoriy Zhurko > https://chemcraftprog.com> > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --000000000000ee38a305e3682817 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thank you Soren, for reminding me why Gregoriy has a fami= liar name .... I have been retired for a few years and no longer do computa= tional chemistry anymore. But I used chemcraft for many years and convinced= collaborators who were not computational chemists to buy copies also, so w= e could communicate well.=C2=A0 So, yes, it is never wrong to be polite and= helpful, and it is never wrong to NOT respond if polite and helpful is not= your thing at the moment.
Steve Williams

<= div class=3D"gmail_quote">
On Sat, Jul= 9, 2022, 6:49 PM Soren Eustis soreneustis|-|g= mail.com <owner-chemistry= (0)ccl.net> wrote:
Hey, be respectful and open to questions from newcomers o= r established scientists.=C2=A0=C2=A0I understood exactly what Grigoriy was= talking about. In this case Grigoriy, happens to have made massive contrib= utions to our community- including coding ChemCraft.=C2=A0=C2=A0

If I were to try to discuss the complexities of the field in any other lang= uage than my native tongue, I=E2=80=99d be at a loss.

Primarily, let=E2=80=99s be better to people here. In this case, Grigoriy i= s a world class scientist who deserves respect. Most importantly, even the = brightest minds need to start somewhere. I spent a lot of time trying to ha= ve questions answered here as a new scientist and some people were pretty h= arsh. Some weren=E2=80=99t. Now I have published many papers and trained ma= ny scientists in the field. Be kind.

Soren=C2=A0
On Jul 9, 2022, 15:01 -0400, Anatoli Kork= in korkin_-_nanoandgiga.com <owner-chemistry(0)ccl.net&= gt;, wrote:

Sent to CCL by: Anatoli Korkin [korkin##nanoandgiga.com]
You should not write a scientific paper without basic understanding of what= you are doing!

Sent from my iPhone

On Jul 9, 2022, at 6:52 AM, Grigoriy Zhurko reg_z= hurko.:.chemcraftprog.com <owner-chemistry*_*ccl.net> wrote:

=EF=BB=BF
Sent to CCL by: "Grigoriy Zhurko" [reg_zhurko()chemcraftprog.com]
Hello,
I compute some molecules with Orca 5.0.3, and the computation sometimes
produces small negative frequencies, despite the symmetry of the molecules = is
C1. If I repeat the computation with another starting point, with some
probability all frequencies are positive.
I found that this problem arises when two additions to the model are added:=
the solvent model (!CPCM(Water)) and additions of some explicit water
molecules to the whole model. I understand that these water molecules produ= ce
very small frequencies along the h-bonds, and these frequencies can become<= br> negative because of some problems with numerical integration. I tried the combination of options !DefGrid3, !TightOpt, !VeryTightSCF, and still
sometimes the negative frequencies are produced. Maybe I need to further increase the computational accuracy with options like "!VeryTightOpt&q= uot;,
"!DefGrid9", UltraTightSCF? I suppose you understand what I mean;= currently
I didn't find the information in the manual, how to further decrease th= e
optimization convergence threshold or increase the accuracy of DFT grid. Please suggest how to do that.
In my work I can avoid using the frequencies since I need mainly the
energies; however I need to explain this somehow in the paper. I suppose, i= t
is not good to compute the entropy of molecules with my keywords, because small frequencies produce big errors with vibrational entropy. So, please suggest me, what should I write in my papers, to explain that it is not goo= d
to compute the Gibbs energy of my molecules, but it is correct to compute a= nd
use the common energy.

Grigoriy Zhurko
= https://chemcraftprog.com>




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