From owner-chemistry@ccl.net Wed Dec 20 23:19:00 2017 From: "Guzman, Francisco fg58-$-njit.edu" To: CCL Subject: CCL:G: Combining Z-matrix with Cartesian coordinates in Gaussian Message-Id: <-53110-171220231326-13195-AC4CxdSv+EXMviQbiEKSuw[a]server.ccl.net> X-Original-From: "Guzman, Francisco" Content-Type: multipart/alternative; boundary="001a113efc28898ad20560d1eb02" Date: Wed, 20 Dec 2017 23:13:19 -0500 MIME-Version: 1.0 Sent to CCL by: "Guzman, Francisco" [fg58%x%njit.edu] --001a113efc28898ad20560d1eb02 Content-Type: text/plain; charset="UTF-8" If you try opt=(modredundant,cartesian) You should see the following error at the end of the output file: ----------------------------------------- Cannot AddRedundant with Cartesian or Z-matrix opts. Error termination via Lnk1e in l1.exe > From the description of your problem, you should be able to use modredundant as a method of freezing a bond/angle/dihedral and relax the rest of the structures by adding the following 1 space after your z-matrix. *Freeze bond between atom 1 & 2:* B 1 2 F *Freeze angle between atom 1 , 2, & 3:* A 1 2 3 F *Freeze dihedral between atom 1 , 2, 3, & 4:* D 1 2 3 4 F This is all with Gaussian 09, Rev. C, At least for Gaussian, I do not know of another way to freeze part of a structure and optimize without using modredundant. On Tue, Dec 19, 2017 at 10:20 AM, Grigoriy Zhurko reg_zhurko# chemcraftprog.com wrote: > > Sent to CCL by: Grigoriy Zhurko [reg_zhurko:chemcraftprog.com] > > > > What are the errors? > > Most atoms are frozen. > > > It's also unclear what you are trying to do. > > Are you trying to do a relaxed scan (PES), rigid scan, or just > > optimize? > > Relaxed PES scan. > > > If it's a relaxed scan, then opt=modredundant is > > required. > > Usually opt=modredundant implies fixing (scanning) a distance, angle or > a dihedral, but I need to fix a distance between a real atom and a dummy > atom between two other real atoms. I don't see how I can specify this > constraint with modreduntant only. > > > I believe for any modredundant job Gaussian internally > > optimizes with a z-matrix only. > > This is strange for me. I found that Z-matrices are a very bad choice for > optimizing rings. > > > Something along the lines of forcing > > the job to optimize using cartesian coordinates, opt=(modredudant, > > cartersian), will not work. > > Are you sure? > > > > > Sincerely, > Grigoriy Zhurko.> > > -- Francisco Guzman PhD Candidate Otto H. York Department of Chemical, Biological and Pharmaceutical Engineering New Jersey Institute of Technology Email: fg58(a)njit.edu, guzman.research(a)gmail.com --001a113efc28898ad20560d1eb02 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
If you try opt=3D(modredundant,cartesian)

You should see the following error at the end of the output file:
=C2=A0-----------------------------------------
=C2=A0Cannot AddR= edundant with Cartesian or Z-matrix opts.
=C2=A0Error termination via Ln= k1e in l1.exe

From the description of your problem, you = should be able to use modredundant as a method of freezing a bond/angle/dih= edral and relax the rest of the structures by adding the following 1 space = after your z-matrix.

Freeze bond between atom 1 & = 2:
B 1 2 F

Freeze angle between atom 1 , 2, &am= p; 3:
A 1 2 3 F

Freeze dihedral between atom 1 = , 2,=C2=A0 3, & 4:
D 1 2 3 4 F

This= is all with Gaussian 09, Rev. C,=C2=A0 At least for Gaussian, I do not kno= w of another way to freeze part of a structure and optimize without using m= odredundant.

On Tue, De= c 19, 2017 at 10:20 AM, Grigoriy Zhurko reg_zhurko#chemcraftprog.com <owner-chemistry(a)ccl.net><= /span> wrote:

Sent to CCL by: Grigoriy Zhurko [reg_zhurko:chemcraftprog.com]


> What are the errors?

=C2=A0 Most atoms are frozen.

> It's also unclear what you are trying to do.
> Are you trying to do a relaxed scan (PES), rigid scan,=C2=A0 or just > optimize?

Relaxed PES scan.

> If it's a relaxed scan, then opt=3Dmodredundant is
> required.

=C2=A0 Usually opt=3Dmodredundant implies fixing (scanning) a distan= ce, angle or a dihedral, but I need to fix a distance between a real atom a= nd a dummy atom between two other real atoms. I don't see how I can spe= cify this constraint with modreduntant only.

>=C2=A0 I believe for any modredundant job Gaussian internally
> optimizes with a z-matrix only.

This is strange for me. I found that Z-matrices are a very bad choic= e for optimizing rings.

> Something along the lines of forcing
> the job to optimize using cartesian coordinates, opt=3D(modredudant, > cartersian), will not work.

Are you sure?




=C2=A0 Sincerely,
=C2=A0 Grigoriy Zhurko.



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--
Franci= sco Guzman
PhD Candidate
Otto H. York Depart= ment of Chemical, Biological and Pharmaceutical Engineering
New Jersey I= nstitute of Technology
--001a113efc28898ad20560d1eb02--