Hi,

indeed - the mix of expert and novi= ce, and of disciplines and approaches, was unique for this list since its s= tart in 1991 with 100 members and the initiative and smarts of Jan Labanows= ki.=C2=A0

Our community has been exemplary in its = self-governance, pioneering in issues like handling commercial announcement= s, the tone of interaction, handling controversies, staying secure, waves o= f technology change from a closed, ASCII-based mailing list many of us read= and wrote on with Pine, to the Web and social media.. See Hocquet, Weber, = and Pisanty,=C2=A0https://jcheminf.biomedcentral.com/articles/10.118= 6/s13321-018-0322-7=C2=A0

Not even the person = who combines the most breadth and depth will be the ultimate expert in ever= ything, and people may choose wisely to ask before delving deep into litera= ture and manuals. The mix of theory and practice is also distinctive of the= CCL like few other virtual communities - and very few are as mature=C2=A0a= s this one in which, as described by other members, utter novices became au= thoritative experts over time and never stopped the flow of good advice.

Cheers,

Alejandro Pisanty

On Sat, Jul 9, 2022 at 8:48 PM Steve Williams willsd*appstate.edu <owner-chemistry]=[ccl.net> wrote:

Thank you Soren, for reminding = me why Gregoriy has a familiar name .... I have been retired for a few year= s and no longer do computational chemistry anymore. But I used chemcraft fo= r many years and convinced collaborators who were not computational chemist= s to buy copies also, so we could communicate well.=C2=A0 So, yes, it is ne= ver 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() 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() ccl.net<= /a>>, 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>

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY() ccl.net or use:
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RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/

- - - - - - - - - - - - - = - - - - - - - - - - - - - -
=C2=A0 =C2=A0 =C2=A0Dr. Alejandro PisantyFacultad de Qu=C3=ADmica UNAM
Av. Universidad 3000, 04510 Mexico DF Mex= ico
+525541444475
Blog: http://pisanty.blogspot.com
LinkedIn: http://www.linkedin.com/in/= pisanty
Unete al grupo UNAM en LinkedIn, http://www.linkedin.com= /e/gis/22285/4A106C0C8614
Twitter: http://twitter.com/apisanty
---->> Un= ete a ISOC Mexico, http:/= /www.isoc.org
. =C2=A0. =C2=A0. =C2=A0. =C2=A0. =C2=A0. =C2=A0. =C2= =A0. =C2=A0. =C2=A0. =C2=A0. =C2=A0. =C2=A0. =C2=A0. =C2=A0. =C2=A0.

<= /div>

--000000000000d9456605e36d7d5a-- From owner-chemistry@ccl.net Sun Jul 10 03:39:00 2022 From: "Neese, Frank neese]![kofo.mpg.de" To: CCL Subject: CCL: [CCL] CCL: Negative frequencies with C1 symmetry (Orca) Message-Id: <-54753-220710033645-22141-0N+2u+buI21hjmn5Exh+nA- -server.ccl.net> X-Original-From: "Neese, Frank" Content-Language: de-DE Content-Type: multipart/alternative; boundary="_000_65519CE448FC44939D162FD3717B9ADFkofompgde_" Date: Sun, 10 Jul 2022 07:36:32 +0000 MIME-Version: 1.0 Sent to CCL by: "Neese, Frank" [neese|a|kofo.mpg.de] --_000_65519CE448FC44939D162FD3717B9ADFkofompgde_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SnVzdCB0byBicmllZmx5IGNsYXJpZnkNCg0KVGlnaHRTQ0YgVGlnaHRPcHQgR3JpZDcgR3JpZHg5 Jw0KDQpJcyBPUkNBIHByZSA1LjAuIHdpdGggNS4wIHRoZXNlIG9sZCBncmlkcyBhcmUgZ29uZSBh bmQgdGhlIG5ldyBncmlkcyBhcmUgbXVjaCBtb3JlIGFjY3VyYXRlIGFuZCBkb27igJh0IG5lZWQg YnVtcGluZyB1cC4NCg0KVGhlIE9QIGhhcyB0cmllZCB0aGVzZSB0aGluZ3MgYW5kIHRoZSBuZWdh 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UlRGSTogPGEgaHJlZj0iaHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9hYm91dGNjbC9pbnN0 cnVjdGlvbnMvIiByZWw9Im5vcmVmZXJyZXIiIHRhcmdldD0iX2JsYW5rIj4NCmh0dHA6Ly93d3cu Y2NsLm5ldC9jaGVtaXN0cnkvYWJvdXRjY2wvaW5zdHJ1Y3Rpb25zLzwvYT48YnI+DQo8YnI+DQo8 YnI+DQo8L2JyPGJyPjwvYnI8YnI+PC9icjxicj1yPGJyPjwvYmxvY2txdW90ZT4NCjwvZGl2Pg0K PC9kaXY+DQo8L2Rpdj4NCjwvYmxvY2txdW90ZT4NCjwvZGl2Pg0KPC9ib2R5Pg0KPC9odG1sPg0K --_000_65519CE448FC44939D162FD3717B9ADFkofompgde_-- From owner-chemistry@ccl.net Sun Jul 10 06:20:00 2022 From: "Sachin Ramesh sachinadityaramesh!^!gmail.com" To: CCL Subject: CCL: [CCL] CCL: Negative frequencies with C1 symmetry (Orca) Message-Id: <-54754-220710061849-30613-kj4ukyes7vJPH4kXa4d9LQ*o*server.ccl.net> X-Original-From: Sachin Ramesh Content-Type: multipart/alternative; boundary="00000000000084e4c605e370c29f" Date: Sun, 10 Jul 2022 15:48:32 +0530 MIME-Version: 1.0 Sent to CCL by: Sachin Ramesh [sachinadityaramesh^gmail.com] --00000000000084e4c605e370c29f Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi, Yes, Prof. Neese. I was referring to ORCA 4.2.1. I should have mentioned it. -Sachin On Sun, Jul 10, 2022 at 3:27 PM Neese, Frank neese]![kofo.mpg.de < owner-chemistry(-)ccl.net> wrote: > Just to briefly clarify > > TightSCF TightOpt Grid7 Gridx9' > > > Is ORCA pre 5.0. with 5.0 these old grids are gone and the new grids are > much more accurate and don=E2=80=98t need bumping up. > > The OP has tried these things and the negative frequencies remained, > meaning that they are not numerical noise. The OP was advised to displace > the molecule along the respective real modes. It was also pointed out to > him that there is a compound script that comes with ORCA 5.0 and later th= at > automatically displaces the molecule along any negative frequency mode > until all negative frequencies are gone. > > That is the best advise I am able to give. > > Sent from my iPad > > On 10. Jul 2022, at 07:56, Sachin Ramesh sachinadityaramesh() gmail.com < > owner-chemistry(-)ccl.net> wrote: > > =EF=BB=BF > Hi, > > Imaginary modes under '-10 cm-1' if not many can be safely ignored. Yo= u > could try to get rid > of the imaginary mode by distorting the structure along the bond, angle o= r > dihedral which is > causing the imaginary mode. > > I should add that imaginary modes are tricky to get rid of when the > solvent correction is used. > The optimization could be done using solvent correction and frequency can > be computed in gas phase. > > 'TightSCF TightOpt Grid7 Gridx9' seems to work for all of our systems > upto 200 atoms, producing > accurate results in good agreement with experimental observations. > > Hope this helps > > with best > - Sachin > > On Sat, Jul 9, 2022 at 7:32 PM 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 th= e >> 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, becaus= e >> small frequencies produce big errors with vibrational entropy. So, pleas= e >> 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 comput= e >> and >> use the common energy. >> >> Grigoriy Zhurko >> https://chemcraftprog.com >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY**ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use>> >> >> --00000000000084e4c605e370c29f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hi,

=C2=A0 Yes, Prof. Neese. I was referring=C2=A0to ORCA 4.2.1.=C2=A0

I should have mentioned it.=C2=A0

-Sachin

On S= un, Jul 10, 2022 at 3:27 PM Neese, Frank neese]![kofo.mpg.de <owner-c= hemistry(-)ccl.net> wrote:

Just to briefly clarify

TightSCF TightOpt Grid7 Gridx9'

Is ORCA pre 5.0. with 5.0 these old grids are gone and the new grids are mu= ch more accurate and don=E2=80=98t need bumping up.=C2=A0

The OP has tried these things and the negative frequencies remained, m= eaning that they are not numerical noise. The OP was advised to displace th= e molecule along the respective real modes. It was also pointed out to him = that there is a compound script that comes with ORCA 5.0 and later that automatically displaces the molecu= le along any negative frequency mode until all negative frequencies are gon= e.=C2=A0

That is the best advise I am able to give.=C2=A0

Sent from my iPad

On 10. Jul 2022, at 07:56, Sachin Ramesh sachinad= ityaramesh() gmail.com &= lt;owner-chemi= stry(-)ccl.net> wrote:

=EF=BB=BF

Hi,

=C2=A0 =C2=A0Imaginary modes under '-10 cm-1' if not many can = be safely ignored. You could try to get rid=C2=A0

of the imaginary mode by distorting the structure along the bond, angl= e or dihedral which is=C2=A0

causing the imaginary mode.=C2=A0

=C2=A0 =C2=A0I should add that imaginary modes are tricky to get rid o= f when the solvent correction is used.=C2=A0

The optimization could be done using solvent correction and frequency = can be computed in gas phase.=C2=A0

=C2=A0 'TightSCF TightOpt Grid7 Gridx9' seems to work for all = of our systems upto 200 atoms, producing=C2=A0

accurate results in good agreement with experimental observations. =C2= =A0

Hope this helps=C2=A0

with best=C2=A0

- Sachin=C2=A0

On Sat, Jul 9, 2022 at 7:32 PM Grigor= iy Zhurko reg_zhurko.:.chemcraftprog.com <owner-chemistry**ccl.net> wrote:

Sent to CCL by: "Grigoriy=C2=A0 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 =
negative because of some problems with numerical integration. I tried the <= br> 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 <= br> small frequencies produce big errors with vibrational entropy. So, please <= br> 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

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY**ccl.net or use:
=C2=A0 =C2=A0 =C2=A0

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--00000000000084e4c605e370c29f-- From owner-chemistry@ccl.net Sun Jul 10 08:11:00 2022 From: "Peter Jarowski peterjarowski_-_gmail.com" To: CCL Subject: CCL: [CCL] CCL: Negative frequencies with C1 symmetry (Orca) Message-Id: <-54755-220710040741-10594-kO4Cxe7wRB1RAi0a1XOSiA=server.ccl.net> X-Original-From: Peter Jarowski Content-Type: multipart/alternative; boundary="0000000000007177df05e36eed71" Date: Sun, 10 Jul 2022 10:07:22 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Jarowski [peterjarowski[*]gmail.com] --0000000000007177df05e36eed71 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi All: A few comments. Do we have a reference for this 10 cm-1 rule-of-thumb? Has anyone published a comparison study using different softwares? I know NWchem ignores lateral frequencies (=C2=AB imaginary frequencies =C2=BB). So careful the outcome m= ight vary even assuming the same implementation of the partition functions. I guess we are talking sub Kcal/mol (cal / mol K :298 K) variations in thermal corrections. For solvatation, its tricky. The hard and fast rule is that the frequencies must be evaluated at the same level as the optimization. Thus, if you optimize in PCM implicit solvent you must do the thermal corrections in solvo as well. It often makes no significant difference, but I imagine it would introduce some small lateral frequencies if you do it in gas phase. In NWChem it requires numerical integration and takes forever. Best regards, Peter On Sun, 10 Jul 2022 at 07:57, Sachin Ramesh sachinadityaramesh() gmail.com = < owner-chemistry:ccl.net> wrote: > Hi, > > Imaginary modes under '-10 cm-1' if not many can be safely ignored. Yo= u > could try to get rid > of the imaginary mode by distorting the structure along the bond, angle o= r > dihedral which is > causing the imaginary mode. > > I should add that imaginary modes are tricky to get rid of when the > solvent correction is used. > The optimization could be done using solvent correction and frequency can > be computed in gas phase. > > 'TightSCF TightOpt Grid7 Gridx9' seems to work for all of our systems > upto 200 atoms, producing > accurate results in good agreement with experimental observations. > > Hope this helps > > with best > - Sachin > > On Sat, Jul 9, 2022 at 7:32 PM 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 th= e >> 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, becaus= e >> small frequencies produce big errors with vibrational entropy. So, pleas= e >> 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 comput= e >> and >> use the common energy. >> >> Grigoriy Zhurko >> https://chemcraftprog.com >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY**ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use>> >> >> --0000000000007177df05e36eed71 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hi All:

A few comments.

Do we = have a reference for this 10 cm-1 rule-of-thumb? Has anyone published a com= parison study using different softwares? I know NWchem ignores lateral freq= uencies (=C2=AB imaginary frequencies =C2=BB). So careful the outcome might= vary even assuming the same implementation of the partition functions. I g= uess we are talking sub Kcal/mol (cal / mol K :298 K) variations in thermal= corrections.

For solvat= ation, its tricky. The hard and fast rule is that the frequencies must be e= valuated at the same level as the optimization. Thus, if you optimize in PC= M implicit solvent you must do the thermal corrections in solvo as well.=C2= =A0 It often makes no significant difference, but I imagine it would introd= uce some small lateral frequencies if you do it in gas phase. In NWChem it = requires numerical integration and takes forever.

Best regards,

Peter

On Sun, 10 Jul 2022 at 07:57, Sachin Ramesh sachi= nadityaramesh() gmail.com <owner-chemistry:ccl.net> wrote:

Hi,

=C2=A0 =C2=A0Imaginary modes under '-10 cm-1' if no= t many can be safely ignored. You could try to get rid=C2=A0
of t= he imaginary mode by distorting the structure along the bond, angle or dihe= dral which is=C2=A0
causing the imaginary mode.=C2=A0
<= br>
=C2=A0 =C2=A0I should add that imaginary modes are tricky to = get rid of when the solvent correction is used.=C2=A0
The optimiz= ation could be done using solvent correction and frequency can be computed = in gas phase.=C2=A0

=C2=A0 'TightSCF TightOpt = Grid7 Gridx9' seems to work for all of our systems upto 200 atoms, prod= ucing=C2=A0
accurate results in good agreement with experimental = observations. =C2=A0

Hope this helps=C2=A0

with best=C2=A0
- Sachin=C2=A0

On Sat, Jul 9, 2022 at 7:32 PM Grigo= riy Zhurko reg_zhurko.:.chemcraftprog.com <owner-chemistry**ccl.net> wrote:

Sent to CCL by: "Grigoriy=C2=A0 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 =
negative because of some problems with numerical integration. I tried the <= br> 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 <= br> small frequencies produce big errors with vibrational entropy. So, please <= br> 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

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY**ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use
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Before posting, check wait time at: http://www.ccl.net

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--0000000000007177df05e36eed71-- From owner-chemistry@ccl.net Sun Jul 10 10:33:00 2022 From: "may abdelghani may01dz : yahoo.fr" To: CCL Subject: CCL: Negative frequencies with C1 symmetry (Orca) Message-Id: <-54756-220710102840-26100-pH5j07/vqVrXZ0xpRDmuqg]![server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="----=_Part_6818212_734716936.1657463311962" Date: Sun, 10 Jul 2022 14:28:31 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz__yahoo.fr] ------=_Part_6818212_734716936.1657463311962 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable I was getting Negative frequencies=C2=A0 whenever I used more than one no= de in the calculations.=C2=A0One of the ORCA users told me that the issue= =C2=A0 with the appearance of the Negative frequencies=C2=A0 came from usin= g more than one node. Of course, those frequencies disappeared right after = I used one node... hope that's your problem. Le dimanche 10 juillet 2022 =C3=A0 09:44:36 UTC+1, Neese, Frank neese]!= [kofo.mpg.de a =C3=A9crit : =20 =20 Just to briefly clarify TightSCF TightOpt Grid7 Gridx9' Is ORCA pre 5.0. with 5.0 these old grids are gone and the new grids are mu= ch more accurate and don=E2=80=98t need bumping up.=C2=A0 The OP has tried these things and the negative frequencies remained, meanin= g that they are not numerical noise. The OP was advised to displace the mol= ecule along the respective real modes. It was also pointed out to him that = there is a compound script that comes with ORCA 5.0 and later that automati= cally displaces the molecule along any negative frequency mode until all ne= gative frequencies are gone.=C2=A0 That is the best advise I am able to give.=C2=A0 Sent from my iPad On 10. Jul 2022, at 07:56, Sachin Ramesh sachinadityaramesh() gmail.com wrote: =EF=BB=BFHi, =C2=A0 =C2=A0Imaginary modes under '-10 cm-1' if not many can be safely ign= ored. You could try to get rid=C2=A0of the imaginary mode by distorting the= structure along the bond, angle or dihedral which is=C2=A0causing the imag= inary mode.=C2=A0 =C2=A0 =C2=A0I should add that imaginary modes are tricky to get rid of whe= n the solvent correction is used.=C2=A0The optimization could be done using= solvent correction and frequency can be computed in gas phase.=C2=A0 =C2=A0 'TightSCF TightOpt Grid7 Gridx9' seems to work for all of our system= s upto 200 atoms, producing=C2=A0accurate results in good agreement with ex= perimental observations. =C2=A0 Hope this helps=C2=A0 with best=C2=A0- Sachin=C2=A0 On Sat, Jul 9, 2022 at 7:32 PM Grigoriy Zhurko reg_zhurko.:.chemcraftprog.c= om wrote: Sent to CCL by: "Grigoriy=C2=A0 Zhurko" [reg_zhurko()chemcraftprog.com] Hello, I compute some molecules with Orca 5.0.3, and the computation sometimes=20 produces small negative frequencies, despite the symmetry of the molecules = is=20 C1. If I repeat the computation with another starting point, with some=20 probability all frequencies are positive. I found that this problem arises when two additions to the model are added:= =20 the solvent model (!CPCM(Water)) and additions of some explicit water=20 molecules to the whole model. I understand that these water molecules produ= ce=20 very small frequencies along the h-bonds, and these frequencies can become= =20 negative because of some problems with numerical integration. I tried the= =20 combination of options !DefGrid3, !TightOpt, !VeryTightSCF, and still=20 sometimes the negative frequencies are produced. Maybe I need to further=20 increase the computational accuracy with options like "!VeryTightOpt",=20 "!DefGrid9", UltraTightSCF? I suppose you understand what I mean; currently= =20 I didn't find the information in the manual, how to further decrease the=20 optimization convergence threshold or increase the accuracy of DFT grid.=20 Please suggest how to do that. In my work I can avoid using the frequencies since I need mainly the=20 energies; however I need to explain this somehow in the paper. I suppose, i= t=20 is not good to compute the entropy of molecules with my keywords, because= =20 small frequencies produce big errors with vibrational entropy. So, please= =20 suggest me, what should I write in my papers, to explain that it is not goo= d=20 to compute the Gibbs energy of my molecules, but it is correct to compute a= nd=20 use the common energy. Grigoriy Zhurko https://chemcraftprog.com -=3D This is automatically added to each message by the mailing script =3D-= =20 E-mail to subscribers: CHEMISTRY**ccl.net or use: =C2=A0 =C2=A0 =C2=A0E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0=20 =20 ------=_Part_6818212_734716936.1657463311962 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

I was getting Negativ= e frequencies whenever I used more than one node in the calculations.=

One of the = ORCA users told me that the issue with the appearance of= the Negative frequencies came from using more than one node. Of cour= se, those frequencies disappeared right after I used one node... hope that'= s your problem.

=20

Le dimanche 10 juillet 2022 =C3=A0 09:44:36 UTC+1, Nees= e, Frank neese]![kofo.mpg.de <owner-chemistry|*|ccl.net> a =C3=A9crit :

Just to briefly clarify

TightSCF TightOpt Grid7 Gridx9'

Is ORCA pre 5.0. with 5.0 these old grids are gone and the new grids are mu= ch more accurate and don=E2=80=98t need bumping up.

The OP has tried these things and the negative frequencies remained, m= eaning that they are not numerical noise. The OP was advised to displace th= e molecule along the respective real modes. It was also pointed out to him = that there is a compound script that comes with ORCA 5.0 and later that automatically displaces the molecu= le along any negative frequency mode until all negative frequencies are gon= e.

That is the best advise I am able to give.

Sent from my iPad

On 10. Jul 2022, at 07:56, Sachin Ramesh sachinad= ityaramesh() gmail.com <owner-chemistry|*|ccl.net> wrote:

=EF=BB=BF

Hi,

Imaginary modes under '-10 cm-1' if not many can be safel= y ignored. You could try to get rid

of the imaginary mode by distorting the structure along the bond, angl= e or dihedral which is

causing the imaginary mode.

I should add that imaginary modes are tricky to get rid o= f when the solvent correction is used.

The optimization could be done using solvent correction and frequency = can be computed in gas phase.

'TightSCF TightOpt Grid7 Gridx9' seems to work for all of our s= ystems upto 200 atoms, producing

accurate results in good agreement with experimental observations. &nb= sp;

Hope this helps

with best

- Sachin

On Sat, Jul 9= , 2022 at 7:32 PM Grigoriy Zhurko reg_zhurko.:.chemcraftprog.co= m <owner-chemistry**ccl.net> wrote:

Sent to CCL by: "Grigoriy Zhurko" [reg_zhurko()chemcraftp= rog.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 =
negative because of some problems with numerical integration. I tried the <= br clear=3D"none"> 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, i= t
is not good to compute the entropy of molecules with my keywords, because <= br clear=3D"none"> small frequencies produce big errors with vibrational entropy. So, please <= br clear=3D"none"> 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

-=3D This is automatically added to each message by the mailing script =3D-= =20
E-mail to subscribers: CHEMISTRY**ccl.net or use:

E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

=20

------=_Part_6818212_734716936.1657463311962-- From owner-chemistry@ccl.net Sun Jul 10 11:28:01 2022 From: "Neese, Frank neese]^[kofo.mpg.de" To: CCL Subject: CCL: [CCL] CCL: Negative frequencies with C1 symmetry (Orca) Message-Id: <-54757-220710100406-21912-brNGcuyqZb4KfyR2R1BrMA/a\server.ccl.net> X-Original-From: "Neese, Frank" Content-Language: de-DE Content-Type: multipart/alternative; boundary="_000_52054C25769F4B0A9E379E9B7316DECEkofompgde_" Date: Sun, 10 Jul 2022 14:03:58 +0000 MIME-Version: 1.0 Sent to CCL by: "Neese, Frank" [neese~!~kofo.mpg.de] --_000_52054C25769F4B0A9E379E9B7316DECEkofompgde_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 U29sdmF0aW9uIGlzIGRvbmUgYW5hbHl0aWNhbGx5IGluIE9SQ0EgaW5jbHVkaW5nIEhlc3NpYW5z IGFuZCBlbXBsb3lpbmcgdGhlIEdhdXNzaWFuIGNoYXJnZSBzY2hlbWUuIEl0IGlzIGVmZmljaWVu dCwgbnVtZXJpY2FsbHkgc21vb3RoIGFuZCBzdGFibGUuDQoNClZvbiBtZWluZW0gaVBob25lIGdl c2VuZGV0DQoNCkFtIDEwLjA3LjIwMjIgdW0gMTU6NTcgc2NocmllYiBQZXRlciBKYXJvd3NraSBw 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