Hello, In Gaussian, unfortunately a relaxed scan can only be done via OPT(ModRedundant), which also means that you cannot use dummy atoms. See the following Q&A for more information: https://chemistry.stackexchange.com/q/49483/4945 You can still perform a rigid scan, but that has to be done via a (symbolic) z-matrix, invoked via the SCAN keyword. E.g.: https://chemistry.stackexchange.com/q/54022/4945 An example for performing a rigid scan with a mixed style coordinates can be found here: https://chemistry.stackexchange.com/q/62886/4945 The z-matrix in your input is, as others pointed out, half frozen. Only the variables in the "Variables" section will actually be optimised, and it will be optimised, not scanned. I am not sure whether the "Constants" section will be treated as constant, because that should require the POPT keyword. E.g.: https://chemistry.stackexchange.com/q/39057/4945 If I understand correctly, you would like to scan the out-of-plane displacement of zinc. The closest to a relaxed scan you can (probably) get is to manually prepare multiple coordinate files where you move the zinc along the z-axis, and freeze all the Zn-N distances with OPT(ModRedundant). Best regards, Martin Am Wed 20/12/2017 um 12:55 AM schrieb Demian Riccardi demianriccardi:gmail.com: > Is it really a valid geometry? From a quick glance at your coordinates, > it appears that all your Z-matrix coordinates are defined, first, > relative to the dummy atom and then all the absolute coordinates come > next. Is it obvious how the two pieces would fit together? You should > make sure your coordinates make sense with what Gaussian expects. > > http://gaussian.com/zmat/ > > > On Tue, Dec 19, 2017 at 6:20 AM, Guzman, Francisco fg58%njit.edu > <http://njit.edu>; <owner-chemistry%a%ccl.net > <mailto:owner-chemistry%a%ccl.net>> wrote: > > What are the errors? It's also unclear what you are trying to do. > Are you trying to do a relaxed scan (PES), rigid scan, or just > optimize? If it's a relaxed scan, then opt=modredundant is > required. I believe for any modredundant job Gaussian internally > optimizes with a z-matrix only. Something along the lines of forcing > the job to optimize using cartesian coordinates, opt=(modredudant, > cartersian), will not work. For a rigid scan (molecule is frozen > except bond/angle/dihedral of interest) use the "scan" keyword > followed by specifying in the z-matrix which angle/bond/dihedral of > interest is to be scanned. Scan also requires the use of a z-matrix. > > I've had many many issues with linear angles myself. If it's just > an optimization, inserting a dummy atom works just fine. However, > for a PES it seems to me that the dummy atom is only considered in > the first step of your scan and is subsequently discarded. Hence, if > a linear angle appears at any place during the scan, my calculations > tend to terminate with something along the lines of error L9999, > "Error linear angle in bend". > > Maybe try another program if this is an issue. NWCHEM could work. > > On Mon, Dec 18, 2017 at 9:34 AM, Grigoriy Zhurko > reg_zhurko||chemcraftprog.com <http://chemcraftprog.com>; > <owner-chemistry|a|ccl.net <mailto:owner-chemistry%7Ca%7Cccl.net>> > wrote: > > > Sent to CCL by: Grigoriy Zhurko [reg_zhurko]~[chemcraftprog.com > <http://chemcraftprog.com>;] > Hello, > > I need to perform a PES scan in Gaussian, so that the distance > between an atom and the center between two other atoms will be > scanned. > When I need to simply scan an iteratomic distance, I use > OPT(MODREDUNDANT). But in current case I have to use a z-matrix > and add a dummy atom (the center between two real atoms). > It is possible to use only Z-matrix for this job, but the result > becomes rather bad: the optimization starts with evident bugs > (probably because this geometry has rings). > I tried to combine the Z-matrix with the Cartesians. I created > the following input file: > > %NPROCSHARED=3 > #P uwB97XD/6-31G(D,P) OPT(Z-Matrix,LOOSE) > NOSYMM > > Silicon > > 0 1 > X > N 1 R12 > X 1 1.400000 2 90.000000 > N 1 R12 3 90.000000 2 180.000000 > N 1 R15 2 A215 3 -90.000000 > N 1 R16 3 A316 5 D5316 > Zn 1 R17 2 A217 5 -D5217 > 6 0.000000000 2.863016000 1.101006000 > 6 0.000000000 2.425840000 2.425840000 > 6 0.000000000 1.101006000 2.863016000 > 1 0.000000000 3.193595000 3.193595000 > 6 0.000000000 2.863016000 -1.101006000 > 6 0.000000000 2.425840000 -2.425840000 > 6 0.000000000 1.101006000 -2.863016000 > 1 0.000000000 3.193595000 -3.193595000 > 6 0.000000000 -1.101006000 -2.863016000 > 6 0.000000000 -2.425840000 -2.425840000 > 6 0.000000000 -2.863016000 -1.101006000 > 1 0.000000000 -3.193595000 -3.193595000 > 6 0.000000000 -2.863016000 1.101006000 > 6 0.000000000 -2.425840000 2.425840000 > 6 0.000000000 -1.101006000 2.863016000 > 1 0.000000000 -3.193595000 3.193595000 > 6 0.000000000 -4.245855000 0.681548000 > 6 0.000000000 -4.245855000 -0.681548000 > 6 0.000000000 -0.681548000 -4.245855000 > 6 0.000000000 0.681548000 -4.245855000 > 6 0.000000000 -0.681548000 4.245855000 > 6 0.000000000 0.681548000 4.245855000 > 6 0.000000000 4.245855000 0.681548000 > 6 0.000000000 4.245855000 -0.681548000 > 1 0.000000000 -5.096481000 1.350466000 > 1 0.000000000 -5.096481000 -1.350466000 > 1 0.000000000 -1.350466000 -5.096481000 > 1 0.000000000 1.350466000 -5.096481000 > 1 0.000000000 5.096481000 -1.350466000 > 1 0.000000000 5.096481000 1.350466000 > 1 0.000000000 -1.350466000 5.096481000 > 1 0.000000000 1.350466000 5.096481000 > Variables: > R12 = 2.04198300 > R15 = 2.04198300 > A215 = 90.00000000 > R16 = 2.04198300 > A316 = 90.00000000 > D5316 = 180.00000000 > A217 = 90.00000000 > D5217 = 90.00000000 > constants > R17 = 0.40000000 s 20 0.2 > > This job constructs a valid geometry, the optimization starts, > but it starts incorrectly: during the optimization, only the > Z-matrix parameters are varied, while the coordinates of most > atoms are fixed. Can I do something to make Gaussian optimize > these atomic coordinates as well? > > > > -= This is automatically added to each message by the mailing > script =-__ > E-mail to subscribers: CHEMISTRY|a|ccl.net > <mailto:CHEMISTRY%7Ca%7Cccl.net> or use: > http://www.ccl.net/cgi-bin/ccl/send_ccl_message > <http://www.ccl.net/cgi-bin/ccl/send_ccl_message>; > > E-mail to administrators: CHEMISTRY-REQUEST|a|ccl.net > <mailto:CHEMISTRY-REQUEST%7Ca%7Cccl.net> or use > http://www.ccl.net/cgi-bin/ccl/send_ccl_message > <http://www.ccl.net/cgi-bin/ccl/send_ccl_message>; > > http://www.ccl.net/chemistry/sub_unsub.shtml > <http://www.ccl.net/chemistry/sub_unsub.shtml>; > > > Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > <http://server.ccl.net/chemistry/announcements/conferences/>; > > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml > <http://www.ccl.net/chemistry/searchccl/index.shtml>; > __ > <http://www.ccl.net/spammers.txt>; > > <http://www.ccl.net/chemistry/aboutccl/instructions/>; > > > > > > -- > Francisco Guzman > PhD Candidate > Otto H. York Department of Chemical, Biological and Pharmaceutical > Engineering > New Jersey Institute of Technology > Email: fg58|a|njit.edu > <mailto:fg58%7Ca%7Cnjit.edu>, guzman.research|a|gmail.com > <mailto:guzman.research%7Ca%7Cgmail.com> > >
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