From owner-chemistry@ccl.net Wed Dec 20 09:52:01 2017
From: "Andreas Klamt klamt|cosmologic.de" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL:G: Computational Science Groups on Facebook and LinkedIn
Message-Id: <-53103-171220014541-9813-i90hOayA0P0ifaeiMe9/mw~!~server.ccl.net>
X-Original-From: Andreas Klamt <klamt*cosmologic.de>
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Sent to CCL by: Andreas Klamt [klamt[]cosmologic.de]
Dear CCL members,

I am now also in the CCL since about 30 years. And I really would love
to see that CCL stays the main communication channel of the
computational chemistry community. It is proven, free of costs, and, as
far as I know, not blocked by any technology all over the world. Many
thanks to Jan for his great work over all the years.

So I like to ask Gabriele Mogni: What is your motivation to start and
promote another alternative channel? It will definitely weeken CCL.
By the way: Is there a technological way to combine them, i.e. to see
the entries of that LinkedIn group in CCL and vice versa?

Nevertheless, let me express some slight (self-)criticism to the CCL
community: The number of interesting discussions in has decreased in the
last years. It is partly a Gaussian support forum. We should have more
interesting and vidid discussions again.

If we want to keep CCL alive, we need to keep it attractive, and start
interesting discussion, not just report a Gaussian error message.
Gaussian has their own support team. They shall care for these messages.
The value of the CCL is that it most likely connects the largest number
of experienced computational chemists. But if we do not share a bit of
our experience in this forum, the younger colleagues, if they are
interested in the experience of the elder at all, have no reason to
follow CCL and will be communicate elsewhere.

Best regards

Andreas









Am 19.12.2017 um 23:13 schrieb Jan Labanowski jkl[A]wowway.biz:
> Sent to CCL by: Jan Labanowski [jkl ~ wowway.biz]
> Dear CCL Members,
> Since some people may be confused... The CCL (Computional Chemistry List) and me personally (Jan Labanowski) are not related in any way to this initiative. I learned about them from CCL like you.
> Jan Labanowski
> CCL Maintainer
> http://www.ccl.net/
> jkl/a\ccl.net>
>
>

-- 

Join us at the 5th-COSMO-RS-Symposium March 2018
Details at www.cosmologic.de/symposium_2018.html
--------------------------------------------------

Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt%x%cosmologic.de
web    	www.cosmologic.de

[University address:      Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt


From owner-chemistry@ccl.net Wed Dec 20 10:27:01 2017
From: "Michel Petitjean petitjean.chiral/a\gmail.com" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: Please join these Computational Science groups on Facebook and LinkedI
Message-Id: <-53104-171220030859-18480-bUPBvRYaGuP9mJoXB1q1bQ _ server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral(~)gmail.com>
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Sent to CCL by: Michel Petitjean [petitjean.chiral() gmail.com]
I agree with David and Andreas.
I do not want to register on facebook or LinkedIn.
Several places to look means wasted time, and I do not evoke privacy
policy, spamming (occurs with LinkedIn), etc.
The CCL is very well managed by Jan and it suffices.
Best regards,
Michel.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral(-)gmail.com (preferred),
        michel.petitjean(-)univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.html

> 2017-12-19 20:39 GMT+03:00 David Mannock dmannock||yahoo.com
> <owner-chemistry()ccl.net>:
>>
>> Agree with Andreas. One site is better than 3! It should have everything in one place and must have a files section. Personally, I do follow CCL, but 3 sites NO! If CCL must be moved to a more modern app for the smartphone generation, it should follow the same format here which is interesting and useful, even for retired geezers like me! It must be searchable from within and from Google. I suggest that before radical moves are made, we discuss what subscribers to CCL want and who will be the Admins for any new site.
>> Given the move towards digital publishing of many social media sites, we also have to look forward to a time when access may require payment. Would a simple cloud listing be better than a social media site? David Mannock
>>
>>
>> On Tuesday, December 19, 2017 2:46 AM, Andreas Klamt klamt|a|cosmologic.de
>> <owner-chemistryÃŒl.net> wrote:
>>
>>
>>
>> Sent to CCL by: Andreas Klamt [klamt+/-cosmologic.de]
>> ... oops, and even more, I see that your group is different from the LinkedIn group
>>
>> Computational Chemistry
>> https://www.linkedin.com/groups/1117927
>>
>> What a pity!!!
>>
>> Andreas
>


From owner-chemistry@ccl.net Wed Dec 20 11:02:01 2017
From: "Martin C. Schwarzer schwarzer{}mail.de" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL:G: Combining Z-matrix with Cartesian coordinates in Gaussian
Message-Id: <-53105-171220092558-1339-sYNBaA8zkwwaJPbJWW3D1Q.:.server.ccl.net>
X-Original-From: "Martin C. Schwarzer" <schwarzer,+,mail.de>
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Sent to CCL by: "Martin C. Schwarzer" [schwarzer!=!mail.de]
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> From: "Martin C. Schwarzer" <schwarzer#mail.de>
To: CCL Subscribers <chemistry#ccl.net>
Message-ID: <48044a4e-fbbf-b873-e10a-99229ead509d#mail.de>
Subject: Re: CCL:G: Combining Z-matrix with Cartesian coordinates in Gaussian
References: <53097-171219105507-3259-ECRg4LaDg3cm/SIQOwak0A#server.ccl.net>
In-Reply-To: <53097-171219105507-3259-ECRg4LaDg3cm/SIQOwak0A#server.ccl.net>

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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?=C2=A0 From a quick glance at your coordi=
nates,
> 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?=C2=A0 You sh=
ould
> make sure your coordinates make sense with what Gaussian expects.
>=20
> http://gaussian.com/zmat/
>=20
>=20
> 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:
>=20
>     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,=C2=A0 or jus=
t
>     optimize? If it's a relaxed scan, then opt=3Dmodredundant is
>     required.=C2=A0 I believe for any modredundant job Gaussian interna=
lly
>     optimizes with a z-matrix only. Something along the lines of forcin=
g
>     the job to optimize using cartesian coordinates, opt=3D(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=
=2E
>=20
>     I've had many many issues with linear angles myself.=C2=A0 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, i=
f
>     a linear angle appears at any place during the scan, my calculation=
s
>     tend to terminate with something along the lines of error L9999,
>     "Error linear angle in bend".=C2=A0
>=20
>     Maybe try another program if this is an issue. NWCHEM could work.
>=20
>     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:
>=20
>=20
>         Sent to CCL by: Grigoriy Zhurko [reg_zhurko]~[chemcraftprog.com=

>         <http://chemcraftprog.com>]
>         Hello,
>=20
>         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 resul=
t
>         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:
>=20
>         %NPROCSHARED=3D3
>         =C2=A0#P uwB97XD/6-31G(D,P) OPT(Z-Matrix,LOOSE)
>         =C2=A0NOSYMM
>=20
>         =C2=A0Silicon
>=20
>         =C2=A00 1
>         =C2=A0X
>         =C2=A0N 1 R12
>         =C2=A0X 1 1.400000 2 90.000000
>         =C2=A0N 1 R12 3 90.000000 2 180.000000
>         =C2=A0N 1 R15 2 A215 3 -90.000000
>         =C2=A0N 1 R16 3 A316 5 D5316
>         =C2=A0Zn 1 R17 2 A217 5 -D5217
>         =C2=A06 0.000000000 2.863016000 1.101006000
>         =C2=A06 0.000000000 2.425840000 2.425840000
>         =C2=A06 0.000000000 1.101006000 2.863016000
>         =C2=A01 0.000000000 3.193595000 3.193595000
>         =C2=A06 0.000000000 2.863016000 -1.101006000
>         =C2=A06 0.000000000 2.425840000 -2.425840000
>         =C2=A06 0.000000000 1.101006000 -2.863016000
>         =C2=A01 0.000000000 3.193595000 -3.193595000
>         =C2=A06 0.000000000 -1.101006000 -2.863016000
>         =C2=A06 0.000000000 -2.425840000 -2.425840000
>         =C2=A06 0.000000000 -2.863016000 -1.101006000
>         =C2=A01 0.000000000 -3.193595000 -3.193595000
>         =C2=A06 0.000000000 -2.863016000 1.101006000
>         =C2=A06 0.000000000 -2.425840000 2.425840000
>         =C2=A06 0.000000000 -1.101006000 2.863016000
>         =C2=A01 0.000000000 -3.193595000 3.193595000
>         =C2=A06 0.000000000 -4.245855000 0.681548000
>         =C2=A06 0.000000000 -4.245855000 -0.681548000
>         =C2=A06 0.000000000 -0.681548000 -4.245855000
>         =C2=A06 0.000000000 0.681548000 -4.245855000
>         =C2=A06 0.000000000 -0.681548000 4.245855000
>         =C2=A06 0.000000000 0.681548000 4.245855000
>         =C2=A06 0.000000000 4.245855000 0.681548000
>         =C2=A06 0.000000000 4.245855000 -0.681548000
>         =C2=A01 0.000000000 -5.096481000 1.350466000
>         =C2=A01 0.000000000 -5.096481000 -1.350466000
>         =C2=A01 0.000000000 -1.350466000 -5.096481000
>         =C2=A01 0.000000000 1.350466000 -5.096481000
>         =C2=A01 0.000000000 5.096481000 -1.350466000
>         =C2=A01 0.000000000 5.096481000 1.350466000
>         =C2=A01 0.000000000 -1.350466000 5.096481000
>         =C2=A01 0.000000000 1.350466000 5.096481000
>         =C2=A0Variables:
>         =C2=A0R12 =3D 2.04198300
>         =C2=A0R15 =3D 2.04198300
>         =C2=A0A215 =3D 90.00000000
>         =C2=A0R16 =3D 2.04198300
>         =C2=A0A316 =3D 90.00000000
>         =C2=A0D5316 =3D 180.00000000
>         =C2=A0A217 =3D 90.00000000
>         =C2=A0D5217 =3D 90.00000000
>         =C2=A0constants
>         =C2=A0R17 =3D 0.40000000 s 20 0.2
>=20
>         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?
>=20
>=20
>=20
>         -=3D This is automatically added to each message by the mailing=

>         script =3D-__
>         E-mail to subscribers: CHEMISTRY|a|ccl.net
>         <mailto:CHEMISTRY%7Ca%7Cccl.net> or use:
>         =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_me=
ssage
>         <http://www.ccl.net/cgi-bin/ccl/send_ccl_message>
>=20
>         E-mail to administrators: CHEMISTRY-REQUEST|a|ccl.net
>         <mailto:CHEMISTRY-REQUEST%7Ca%7Cccl.net> or use
>         =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_me=
ssage
>         <http://www.ccl.net/cgi-bin/ccl/send_ccl_message>
>=20>         =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_unsub.sht=
ml
>         <http://www.ccl.net/chemistry/sub_unsub.shtml>
>=20>=20>         Conferences:
>         http://server.ccl.net/chemistry/announcements/conferences/
>         <http://server.ccl.net/chemistry/announcements/conferences/>
>=20
>         Search Messages:
>         http://www.ccl.net/chemistry/searchccl/index.shtml
>         <http://www.ccl.net/chemistry/searchccl/index.shtml>
>         __ =C2=A0 =C2=A0 =C2=A0>         <http://www.ccl.net/spammers.txt>
>=20>         <http://www.ccl.net/chemistry/aboutccl/instructions/>
>=20
>=20
>=20
>=20
>=20
>     --=20
>     Francisco Guzman
>     PhD Candidate
>     Otto H. York Department of Chemical, Biological and Pharmaceutical
>     Engineering
>     New Jersey Institute of Technology
>     Email:=C2=A0fg58|a|njit.edu
>     <mailto:fg58%7Ca%7Cnjit.edu>,=C2=A0guzman.research|a|gmail.com
>     <mailto:guzman.research%7Ca%7Cgmail.com>
>=20
>=20


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From owner-chemistry@ccl.net Wed Dec 20 13:01:00 2017
From: "Judith Rommel jbr36++cam.ac.uk" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: Please join these Computational Science groups on Facebook and LinkedI
Message-Id: <-53106-171220120310-23490-LX5aV4xwimDbvA+RIKWjJQ__server.ccl.net>
X-Original-From: Judith Rommel <jbr36]=[cam.ac.uk>
Content-Language: en-US
Content-Transfer-Encoding: 8bit
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Date: Wed, 20 Dec 2017 17:03:00 +0000
MIME-Version: 1.0


Sent to CCL by: Judith Rommel [jbr36:_:cam.ac.uk]
Dear all,

clearly there are advantages in having both the well managed CCL list
and social media groups to meet and discuss.
We may have different preferences depending on which generation we come
> from.
https://www.entrepreneur.com/article/228029
Having both connects the generations of researchers and offers the
choice for each preference.

Best wishes,
Judith Rommel



On 20/12/2017 08:08, Michel Petitjean petitjean.chiral/agmail.com wrote:
> Sent to CCL by: Michel Petitjean [petitjean.chiral() gmail.com]
> I agree with David and Andreas.
> I do not want to register on facebook or LinkedIn.
> Several places to look means wasted time, and I do not evoke privacy
> policy, spamming (occurs with LinkedIn), etc.
> The CCL is very well managed by Jan and it suffices.
> Best regards,
> Michel.
>
> Michel Petitjean
> MTi, INSERM UMR-S 973, University Paris 7,
> 35 rue Helene Brion, 75205 Paris Cedex 13, France.
> Phone: +331 5727 8434; Fax: +331 5727 8372
> E-mail: petitjean.chiral,,gmail.com (preferred),
>         michel.petitjean,,univ-paris-diderot.fr
> http://petitjeanmichel.free.fr/itoweb.petitjean.html
>
>> 2017-12-19 20:39 GMT+03:00 David Mannock dmannock||yahoo.com
>> <owner-chemistry()ccl.net>:
>>> Agree with Andreas. One site is better than 3! It should have everything in one place and must have a files section. Personally, I do follow CCL, but 3 sites NO! If CCL must be moved to a more modern app for the smartphone generation, it should follow the same format here which is interesting and useful, even for retired geezers like me! It must be searchable from within and from Google. I suggest that before radical moves are made, we discuss what subscribers to CCL want and who will be the Admins for any new site.
>>> Given the move towards digital publishing of many social media sites, we also have to look forward to a time when access may require payment. Would a simple cloud listing be better than a social media site? David Mannock
>>>
>>>
>>> On Tuesday, December 19, 2017 2:46 AM, Andreas Klamt klamt|a|cosmologic.de
>>> <owner-chemistryÃŒl.net> wrote:
>>>
>>>
>>>
>>> Sent to CCL by: Andreas Klamt [klamt+/-cosmologic.de]
>>> ... oops, and even more, I see that your group is different from the LinkedIn group
>>>
>>> Computational Chemistry
>>> https://www.linkedin.com/groups/1117927
>>>
>>> What a pity!!!
>>>
>>> Andreas

-- 
Dr. Judith B. Rommel
Department of Chemistry
University of Cambridge
Lensfield Road, Cambridge, CB2 1EW

http://people.ds.cam.ac.uk/jbr36
Twitter: :+:jbr_sience
Email: jbr36:+:cam.ac.uk


From owner-chemistry@ccl.net Wed Dec 20 13:36:00 2017
From: "Brian Skinn bskinn . alum.mit.edu" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL:G: Computational Science Groups on Facebook and LinkedIn
Message-Id: <-53107-171220124403-11073-c0SWPCd73hqp/EANlBIc1g*server.ccl.net>
X-Original-From: Brian Skinn <bskinn_._alum.mit.edu>
Content-Type: multipart/alternative; boundary="94eb2c1a303aadca1b0560c920a1"
Date: Wed, 20 Dec 2017 12:43:36 -0500
MIME-Version: 1.0


Sent to CCL by: Brian Skinn [bskinn : alum.mit.edu]
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All,

In the last couple of years there has been quite a bit of activity in the
quantum/computational chemistry realm on Chemistry Stack Exchange (
https://chemistry.stackexchange.com).  Representative questions/answers can
be found in, e.g., the quantum-chemistry (https://chemistry.stackexchan
ge.com/questions/tagged/quantum-chemistry) and computational-chemistry (
https://chemistry.stackexchange.com/questions/tagged/computational-chemistr=
y
).

While I recognize that this Chem.SE activity contributes to the 'dilution'
of the community, it provides a forum for a completely different kind of
interaction than is afforded by CCL: detailed exposition of technical
questions and answers, and interactions closer to real-time via the Q&A,
the comments thereon, and the chat rooms associated with the site (
https://chat.stackexchange.com/?tab=3Dsite&host=3Dchemistry.stackexchange.c=
om).


I recognize and applaud the impulse to try to retain a single "canonical"
channel of discussion for the community, and the unity it would bring, but
I fear it's a quixotic errand. I don't see how this (or any) community can
avoid the fragmentation occurring pretty much everywhere else in the
digital world.  Younger people are now accustomed to faster communication,
purpose-tuned tools (often "microtools"), and extensive customizability in
their communities; beseeching them not to branch out into fora more aligned
with the way they work and think is not likely to have much of an effect.
Figuring out a way to connect/integrate CCL with these other spheres is
likely to be much more effective at keeping it relevant to younger
scientists.

Examples include automatic posting to CCL of:

 - New Chem.SE questions tagged with quantum/computational chemistry
(perhaps only after they've reached a minimum upvote threshold)
 - Digests of discussion threads on LinkedIn/Facebook/other groups
 - Tie-ins to ResearchGate/other publication sites

Obviously I don't expect all of this to fall on our august list manager.
These are all things that the community could develop, and integrate with
Jan's support/blessing.  I unfortunately don't really know how to implement
any of these above things myself, though, without significant further
research.

CCL *has* to innovate, if it is not to fade away slowly into irrelevance.


-Brian


On Wed, Dec 20, 2017 at 1:45 AM, Andreas Klamt klamt|cosmologic.de <
owner-chemistry]_[ccl.net> wrote:

>
> Sent to CCL by: Andreas Klamt [klamt[]cosmologic.de]
> Dear CCL members,
>
> I am now also in the CCL since about 30 years. And I really would love
> to see that CCL stays the main communication channel of the
> computational chemistry community. It is proven, free of costs, and, as
> far as I know, not blocked by any technology all over the world. Many
> thanks to Jan for his great work over all the years.
>
> So I like to ask Gabriele Mogni: What is your motivation to start and
> promote another alternative channel? It will definitely weeken CCL.
> By the way: Is there a technological way to combine them, i.e. to see
> the entries of that LinkedIn group in CCL and vice versa?
>
> Nevertheless, let me express some slight (self-)criticism to the CCL
> community: The number of interesting discussions in has decreased in the
> last years. It is partly a Gaussian support forum. We should have more
> interesting and vidid discussions again.
>
> If we want to keep CCL alive, we need to keep it attractive, and start
> interesting discussion, not just report a Gaussian error message.
> Gaussian has their own support team. They shall care for these messages.
> The value of the CCL is that it most likely connects the largest number
> of experienced computational chemists. But if we do not share a bit of
> our experience in this forum, the younger colleagues, if they are
> interested in the experience of the elder at all, have no reason to
> follow CCL and will be communicate elsewhere.
>
> Best regards
>
> Andreas
>
>
>
>
>
>
>
>
>
> Am 19.12.2017 um 23:13 schrieb Jan Labanowski jkl[A]wowway.biz:
> > Sent to CCL by: Jan Labanowski [jkl ~ wowway.biz]
> > Dear CCL Members,
> > Since some people may be confused... The CCL (Computional Chemistry
> List) and me personally (Jan Labanowski) are not related in any way to th=
is
> initiative. I learned about them from CCL like you.
> > Jan Labanowski
> > CCL Maintainer
> > http://www.ccl.net/
> > jkl/a\ccl.net>
> >
> >
>
> --
>
> Join us at the 5th-COSMO-RS-Symposium March 2018
> Details at www.cosmologic.de/symposium_2018.html
> --------------------------------------------------
>
> Prof. Dr. Andreas Klamt
> CEO / Gesch=C3=A4ftsf=C3=BChrer
> COSMOlogic GmbH & Co. KG
> Imbacher Weg 46
> D-51379 Leverkusen, Germany
>
> phone   +49-2171-731681
> fax     +49-2171-731689
> e-mail  klamt*_*cosmologic.de
> web     www.cosmologic.de
>
> [University address:      Inst. of Physical and
> Theoretical Chemistry, University of Regensburg]
>
> HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
> Komplementaer: COSMOlogic Verwaltungs GmbH
> HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
>
>
>
> -=3D This is automatically added to each message by the mailing script =
=3D->
>
>

--94eb2c1a303aadca1b0560c920a1
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr">All,<div><br></div><div>In the last couple of years there =
has been quite a bit of activity in the quantum/computational chemistry rea=
lm on Chemistry Stack Exchange (<a href=3D"https://chemistry.stackexchange.=
com" target=3D"_blank">https://chemistry.stackexchan<wbr>ge.com</a>).=C2=A0=
 Representative questions/answers can be found in, e.g., the quantum-chemis=
try (<a href=3D"https://chemistry.stackexchange.com/questions/tagged/quantu=
m-chemistry" target=3D"_blank">https://chemistry.stackexchan<wbr>ge.com/que=
stions/tagged/<wbr>quantum-chemistry</a>)=C2=A0and computational-chemistry =
(<a href=3D"https://chemistry.stackexchange.com/questions/tagged/computatio=
nal-chemistry" target=3D"_blank">https://chemistry.stackexchan<wbr>ge.com/q=
uestions/tagged/<wbr>computational-chemistry</a>).</div><div><br></div><div=
>While I recognize that this Chem.SE activity contributes to the &#39;dilut=
ion&#39; of the community, it provides a forum for a completely different k=
ind of interaction than is afforded by CCL: detailed exposition of technica=
l questions and answers, and interactions closer to real-time via the Q&amp=
;A, the comments thereon, and the chat rooms associated with the site (<a h=
ref=3D"https://chat.stackexchange.com/?tab=3Dsite&amp;host=3Dchemistry.stac=
kexchange.com" target=3D"_blank">https://chat.stackexchange.co<wbr>m/?tab=
=3Dsite&amp;host=3Dchemistry.sta<wbr>ckexchange.com</a>).</div><div><br></d=
iv><div><br></div><div>I recognize and applaud the impulse to try to retain=
 a single &quot;canonical&quot; channel of discussion for the community, an=
d the unity it would bring, but I fear it&#39;s a quixotic errand. I don&#3=
9;t see how this (or any) community can avoid the fragmentation occurring p=
retty much everywhere else in the digital world.=C2=A0 Younger people are n=
ow accustomed to faster communication, purpose-tuned tools (often &quot;mic=
rotools&quot;), and extensive customizability in their communities; beseech=
ing them not to branch out into fora more aligned with the way they work an=
d think is not likely to have much of an effect.=C2=A0 Figuring out a way t=
o connect/integrate CCL with these other spheres is likely to be much more =
effective at keeping it relevant to younger scientists.</div><div><br></div=
><div>Examples include automatic posting to CCL of:</div><div><br></div><di=
v>=C2=A0- New Chem.SE questions tagged with quantum/computational chemistry=
 (perhaps only after they&#39;ve reached a minimum upvote threshold)</div><=
div>=C2=A0- Digests of discussion threads on LinkedIn/Facebook/other groups=
</div><div>=C2=A0- Tie-ins to ResearchGate/other publication sites</div><di=
v><br></div><div>Obviously I don&#39;t expect all of this to fall on our au=
gust list manager.=C2=A0 These are all things that the community could deve=
lop, and integrate with Jan&#39;s support/blessing.=C2=A0 I unfortunately d=
on&#39;t really know how to implement any of these above things myself, tho=
ugh, without significant further research.</div><div><br></div><div>CCL *ha=
s* to innovate, if it is not to fade away slowly into irrelevance.</div><di=
v><br></div><div><br></div><div>-Brian</div><div><br></div></div><div class=
=3D"gmail_extra"><br><div class=3D"gmail_quote">On Wed, Dec 20, 2017 at 1:4=
5 AM, Andreas Klamt klamt|<a href=3D"http://cosmologic.de">cosmologic.de</a=
> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry]_[ccl.net" target=
=3D"_blank">owner-chemistry]_[ccl.net</a>&gt;</span> wrote:<br><blockquote cl=
ass=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;p=
adding-left:1ex"><br>
Sent to CCL by: Andreas Klamt [klamt[]<a href=3D"http://cosmologic.de" rel=
=3D"noreferrer" target=3D"_blank">cosmologic.de</a>]<br>
Dear CCL members,<br>
<br>
I am now also in the CCL since about 30 years. And I really would love<br>
to see that CCL stays the main communication channel of the<br>
computational chemistry community. It is proven, free of costs, and, as<br>
far as I know, not blocked by any technology all over the world. Many<br>
thanks to Jan for his great work over all the years.<br>
<br>
So I like to ask Gabriele Mogni: What is your motivation to start and<br>
promote another alternative channel? It will definitely weeken CCL.<br>
By the way: Is there a technological way to combine them, i.e. to see<br>
the entries of that LinkedIn group in CCL and vice versa?<br>
<br>
Nevertheless, let me express some slight (self-)criticism to the CCL<br>
community: The number of interesting discussions in has decreased in the<br=
>
last years. It is partly a Gaussian support forum. We should have more<br>
interesting and vidid discussions again.<br>
<br>
If we want to keep CCL alive, we need to keep it attractive, and start<br>
interesting discussion, not just report a Gaussian error message.<br>
Gaussian has their own support team. They shall care for these messages.<br=
>
The value of the CCL is that it most likely connects the largest number<br>
of experienced computational chemists. But if we do not share a bit of<br>
our experience in this forum, the younger colleagues, if they are<br>
interested in the experience of the elder at all, have no reason to<br>
follow CCL and will be communicate elsewhere.<br>
<br>
Best regards<br>
<br>
Andreas<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
Am 19.12.2017 um 23:13 schrieb Jan Labanowski jkl[A]<a href=3D"http://wowwa=
y.biz" rel=3D"noreferrer" target=3D"_blank">wowway.biz</a>:<br>
&gt; Sent to CCL by: Jan Labanowski [jkl ~ <a href=3D"http://wowway.biz" re=
l=3D"noreferrer" target=3D"_blank">wowway.biz</a>]<br>
&gt; Dear CCL Members,<br>
&gt; Since some people may be confused... The CCL (Computional Chemistry Li=
st) and me personally (Jan Labanowski) are not related in any way to this i=
nitiative. I learned about them from CCL like you.<br>
&gt; Jan Labanowski<br>
&gt; CCL Maintainer<br>
&gt; <a href=3D"http://www.ccl.net/" rel=3D"noreferrer" target=3D"_blank">h=
ttp://www.ccl.net/</a><br>
&gt; jkl/a\<a href=3D"http://ccl.net" rel=3D"noreferrer" target=3D"_blank">=
ccl.net</a>&gt;<br>
&gt;<br>
&gt;<br>
<br>
--<br>
<br>
Join us at the 5th-COSMO-RS-Symposium March 2018<br>
Details at <a href=3D"http://www.cosmologic.de/symposium_2018.html" rel=3D"=
noreferrer" target=3D"_blank">www.cosmologic.de/symposium_<wbr>2018.html</a=
><br>
------------------------------<wbr>--------------------<br>
<br>
Prof. Dr. Andreas Klamt<br>
CEO / Gesch=C3=A4ftsf=C3=BChrer<br>
COSMOlogic GmbH &amp; Co. KG<br>
Imbacher Weg 46<br>
D-51379 Leverkusen, Germany<br>
<br>
phone=C2=A0 =C2=A0<a href=3D"tel:%2B49-2171-731681" value=3D"+492171731681"=
>+49-2171-731681</a><br>
fax=C2=A0 =C2=A0 =C2=A0<a href=3D"tel:%2B49-2171-731689" value=3D"+49217173=
1689">+49-2171-731689</a><br>
e-mail=C2=A0 klamt*_*<a href=3D"http://cosmologic.de" rel=3D"noreferrer" ta=
rget=3D"_blank">cosmologic.de</a><br>
web=C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.cosmologic.de" rel=3D"noreferr=
er" target=3D"_blank">www.cosmologic.de</a><br>
<br>
[University address:=C2=A0 =C2=A0 =C2=A0 Inst. of Physical and<br>
Theoretical Chemistry, University of Regensburg]<br>
<br>
HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt<br>
Komplementaer: COSMOlogic Verwaltungs GmbH<br>
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt<br>
<br>
<br>
<br>
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>searchccl/index.shtml</a><br>
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l/instructions/</a><br>
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<br>
</blockquote></div><br></div>

--94eb2c1a303aadca1b0560c920a1--


From owner-chemistry@ccl.net Wed Dec 20 14:11:00 2017
From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor^fluor.quimica.uniovi.es" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL: Please join these Computational Science groups on Facebook and LinkedI
Message-Id: <-53108-171220125050-12456-fNepvFDDrYlCO3lYNImSxg],[server.ccl.net>
X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal <victor]=[fluor.quimica.uniovi.es>
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Wed, 20 Dec 2017 17:53:55 +0100
MIME-Version: 1.0


Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor[-]fluor.quimica.uniovi.es]
On Wed, Dec 20, 2017 at 09:08:52AM +0100, Michel Petitjean petitjean.chiral/agmail.com wrote:
> 
> Sent to CCL by: Michel Petitjean [petitjean.chiral() gmail.com]
> I agree with David and Andreas.
> I do not want to register on facebook or LinkedIn.
> Several places to look means wasted time, and I do not evoke privacy
> policy, spamming (occurs with LinkedIn), etc.
> The CCL is very well managed by Jan and it suffices.
> Best regards,

Hi,

I subscribe totally the opinion of Michel Petitjean. Every new social
platform is an unwelcome distraction or worse. Researchgate, for instance
had the unpleasent tradition to present themselves impersonating a
friend and modifying the e-mail to their web address when submitting
anibody a reprint.

So, ccl oldtime e-mail is far better than Linkedin, facebook or whatever
social media you may defend.

My clear opinion,
                 Víctor Luaña
--
    .  .    "Never let your sense of morals prevent you from doing
   / `' \     what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \   'Tis the time's plague when madmen lead the blind.
|  \'`'`/  |    The tragedy of King Lear (act IV,scene 1)
|  |'`'`|  | 
 \/`'`'`'\/
==(((==)))===================================+===========================
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:  <victor-.-fluor.quimica.uniovi.es>  !
! phone: +34-985-103491  fax: +34-985-103125 !
+--------------------------------------------+
 GroupPage: <http://azufre.quimica.uniovi.es/>
 Articles:  <http://scholar.google.com/citations?user=Ibl1BWAAAAAJ&hl=es>
 git-hub:   <https://github.com/aoterodelaroza>
 ORCID: 0000-0003-4585-4627; RID: H-2045-2015


From owner-chemistry@ccl.net Wed Dec 20 14:46:00 2017
From: "David Mannock dmannock++yahoo.com" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: Please join these Computational Science groups on Facebook and LinkedI
Message-Id: <-53109-171220132123-25505-vIWXtALq11HKvK9kGOehSg|*|server.ccl.net>
X-Original-From: David Mannock <dmannock-x-yahoo.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_1995362_1615005477.1513794061654"
Date: Wed, 20 Dec 2017 18:21:01 +0000 (UTC)
MIME-Version: 1.0


Sent to CCL by: David Mannock [dmannock^^^yahoo.com]
------=_Part_1995362_1615005477.1513794061654
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

Agreed! I also joined several other relevant QC groups that came up on Face=
book in a scrolling window, but have not examined them closely. I think tha=
t a central list like CCL is most useful for technical questions. Again I'l=
l mention that eventually a cloud based app may be a good future option. I'=
ve had a hobby related resource account on issuu.com for several years. On =
that site, pdf downloads are free. Giving the public free access to my univ=
ersity account was not an option. David =20

    On Wednesday, December 20, 2017 10:35 AM, Michel Petitjean petitjean.ch=
iral/agmail.com <owner-chemistry..ccl.net> wrote:
=20

=20
Sent to CCL by: Michel Petitjean [petitjean.chiral() gmail.com]
I agree with David and Andreas.
I do not want to register on facebook or LinkedIn.
Several places to look means wasted time, and I do not evoke privacy
policy, spamming (occurs with LinkedIn), etc.
The CCL is very well managed by Jan and it suffices.
Best regards,
Michel.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral,,gmail.com (preferred),
=C2=A0 =C2=A0 =C2=A0 =C2=A0 michel.petitjean,,univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.html

> 2017-12-19 20:39 GMT+03:00 David Mannock dmannock||yahoo.com
> <owner-chemistry()ccl.net>:
>>
>> Agree with Andreas. One site is better than 3! It should have everything=
 in one place and must have a files section. Personally, I do follow CCL, b=
ut 3 sites NO! If CCL must be moved to a more modern app for the smartphone=
 generation, it should follow the same format here which is interesting and=
 useful, even for retired geezers like me! It must be searchable from withi=
n and from Google. I suggest that before radical moves are made, we discuss=
 what subscribers to CCL want and who will be the Admins for any new site.
>> Given the move towards digital publishing of many social media sites, we=
 also have to look forward to a time when access may require payment. Would=
 a simple cloud listing be better than a social media site? David Mannock
>>
>>
>> On Tuesday, December 19, 2017 2:46 AM, Andreas Klamt klamt|a|cosmologic.=
de
>> <owner-chemistry=C3=8Cl.net> wrote:
>>
>>
>>
>> Sent to CCL by: Andreas Klamt [klamt+/-cosmologic.de]
>> ... oops, and even more, I see that your group is different from the Lin=
kedIn group
>>
>> Computational Chemistry
>> https://www.linkedin.com/groups/1117927
>>
>> What a pity!!!
>>
>> Andreas
>



-=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20
=C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0=20
------=_Part_1995362_1615005477.1513794061654
Content-Type: text/html; charset=UTF-8
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<html><head></head><body><div style=3D"color:#000; background-color:#fff; f=
ont-family:garamond, new york, times, serif;font-size:16px"><div id=3D"yui_=
3_16_0_ym19_1_1513793271948_21229" dir=3D"ltr"><span id=3D"yui_3_16_0_ym19_=
1_1513793271948_21258">Agreed! I also joined several other relevant QC grou=
ps that came up on Facebook in a scrolling window, but have not examined th=
em closely. I think that a central list like CCL is most useful for technic=
al questions. Again I'll mention that eventually a cloud based app may be a=
 good future option. I've had a hobby related resource account on issuu.com=
 for several years. On that site, pdf downloads are free. Giving the public=
 free access to my university account was not an option. David </span></div=
> <div class=3D"qtdSeparateBR"><br><br></div><div class=3D"yahoo_quoted" st=
yle=3D"display: block;"> <div style=3D"font-family: garamond, new york, tim=
es, serif; font-size: 16px;"> <div style=3D"font-family: HelveticaNeue, Hel=
vetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"=
> <div dir=3D"ltr"><font face=3D"Arial" size=3D"2"> On Wednesday, December =
20, 2017 10:35 AM, Michel Petitjean petitjean.chiral/agmail.com &lt;owner-c=
hemistry..ccl.net&gt; wrote:<br></font></div>  <br><br> <div class=3D"y_msg_=
container"><div dir=3D"ltr"><br></div><div dir=3D"ltr">Sent to CCL by: Mich=
el Petitjean [petitjean.chiral() gmail.com]<br></div><div dir=3D"ltr">I agr=
ee with David and Andreas.<br></div><div dir=3D"ltr">I do not want to regis=
ter on facebook or LinkedIn.<br></div><div dir=3D"ltr">Several places to lo=
ok means wasted time, and I do not evoke privacy<br></div><div dir=3D"ltr">=
policy, spamming (occurs with LinkedIn), etc.<br></div><div dir=3D"ltr">The=
 CCL is very well managed by Jan and it suffices.<br></div><div dir=3D"ltr"=
>Best regards,<br></div><div dir=3D"ltr">Michel.<br></div><div dir=3D"ltr">=
<br></div><div dir=3D"ltr">Michel Petitjean<br></div><div dir=3D"ltr">MTi, =
INSERM UMR-S 973, University Paris 7,<br></div><div dir=3D"ltr">35 rue Hele=
ne Brion, 75205 Paris Cedex 13, France.<br></div><div dir=3D"ltr">Phone: +3=
31 5727 8434; Fax: +331 5727 8372<br></div><div dir=3D"ltr">E-mail: petitje=
an.chiral,,gmail.com (preferred),<br></div><div dir=3D"ltr">&nbsp; &nbsp; &=
nbsp; &nbsp; michel.petitjean,,univ-paris-diderot.fr<br></div><div dir=3D"l=
tr"><a href=3D"http://petitjeanmichel.free.fr/itoweb.petitjean.html" target=
=3D"_blank">http://petitjeanmichel.free.fr/itoweb.petitjean.html</a><br></d=
iv><div dir=3D"ltr"><br></div><div dir=3D"ltr">&gt; 2017-12-19 20:39 GMT+03=
:00 David Mannock dmannock||yahoo.com<br></div><div dir=3D"ltr">&gt; &lt;ow=
ner-chemistry()ccl.net&gt;:<br></div><div dir=3D"ltr">&gt;&gt;<br></div><di=
v dir=3D"ltr">&gt;&gt; Agree with Andreas. One site is better than 3! It sh=
ould have everything in one place and must have a files section. Personally=
, I do follow CCL, but 3 sites NO! If CCL must be moved to a more modern ap=
p for the smartphone generation, it should follow the same format here whic=
h is interesting and useful, even for retired geezers like me! It must be s=
earchable from within and from Google. I suggest that before radical moves =
are made, we discuss what subscribers to CCL want and who will be the Admin=
s for any new site.<br></div><div dir=3D"ltr">&gt;&gt; Given the move towar=
ds digital publishing of many social media sites, we also have to look forw=
ard to a time when access may require payment. Would a simple cloud listing=
 be better than a social media site? David Mannock<br></div><div dir=3D"ltr=
">&gt;&gt;<br></div><div dir=3D"ltr">&gt;&gt;<br></div><div dir=3D"ltr">&gt=
;&gt; On Tuesday, December 19, 2017 2:46 AM, Andreas Klamt klamt|a|cosmolog=
ic.de<br></div><div dir=3D"ltr">&gt;&gt; &lt;owner-chemistry=C3=8Cl.net&gt;=
 wrote:<br></div><div dir=3D"ltr">&gt;&gt;<br></div><div dir=3D"ltr">&gt;&g=
t;<br></div><div dir=3D"ltr">&gt;&gt;<br></div><div dir=3D"ltr">&gt;&gt; Se=
nt to CCL by: Andreas Klamt [klamt+/-cosmologic.de]<br></div><div dir=3D"lt=
r">&gt;&gt; ... oops, and even more, I see that your group is different fro=
m the LinkedIn group<br></div><div dir=3D"ltr">&gt;&gt;<br></div><div dir=
=3D"ltr">&gt;&gt; Computational Chemistry<br></div><div dir=3D"ltr">&gt;&gt=
; <a href=3D"https://www.linkedin.com/groups/1117927" target=3D"_blank">htt=
ps://www.linkedin.com/groups/1117927</a><br></div><div dir=3D"ltr">&gt;&gt;=
<br></div><div dir=3D"ltr">&gt;&gt; What a pity!!!<br></div><div dir=3D"ltr=
">&gt;&gt;<br></div><div dir=3D"ltr">&gt;&gt; Andreas<br></div><div dir=3D"=
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From owner-chemistry@ccl.net Wed Dec 20 23:19:00 2017
From: "Guzman, Francisco fg58-$-njit.edu" <owner-chemistry[a]server.ccl.net>
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" <fg58#%#njit.edu>
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 <owner-chemistry(a)ccl.net> 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
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Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><div>If you try opt=3D(modredundant,cartesian) <br><br></d=
iv>You should see the following error at the end of the output file:<br><di=
v><div>=C2=A0-----------------------------------------<br>=C2=A0Cannot AddR=
edundant with Cartesian or Z-matrix opts.<br>=C2=A0Error termination via Ln=
k1e in l1.exe <br><br></div><div>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.<br><br></div><div><b>Freeze bond between atom 1 &amp; =
2:<br></b></div><div>B 1 2 F<br><br><b>Freeze angle between atom 1 , 2, &am=
p; 3:<br></b></div><div>A 1 2 3 F<br><br><b>Freeze dihedral between atom 1 =
, 2,=C2=A0 3, &amp; 4:<br></b></div><div>D 1 2 3 4 F<br><br></div><div>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.<br></div><div><b></b></div><div><b></b></div><div><b></b></div=
></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Tue, De=
c 19, 2017 at 10:20 AM, Grigoriy Zhurko reg_zhurko#<a href=3D"http://chemcr=
aftprog.com">chemcraftprog.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:=
owner-chemistry(a)ccl.net" target=3D"_blank">owner-chemistry(a)ccl.net</a>&gt;<=
/span> wrote:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8=
ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Sent to CCL by: Grigoriy Zhurko [reg_zhurko:<a href=3D"http://chemcraftprog=
.com" rel=3D"noreferrer" target=3D"_blank">chemcraftprog.com</a>]<br>
<br>
<br>
&gt; What are the errors?<br>
<br>
=C2=A0 Most atoms are frozen.<br>
<span class=3D""><br>
&gt; It&#39;s also unclear what you are trying to do.<br>
&gt; Are you trying to do a relaxed scan (PES), rigid scan,=C2=A0 or just<b=
r>
&gt; optimize?<br>
<br>
</span>Relaxed PES scan.<br>
<span class=3D""><br>
&gt; If it&#39;s a relaxed scan, then opt=3Dmodredundant is<br>
&gt; required.<br>
<br>
</span>=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&#39;t see how I can spe=
cify this constraint with modreduntant only.<br>
<span class=3D""><br>
&gt;=C2=A0 I believe for any modredundant job Gaussian internally<br>
&gt; optimizes with a z-matrix only.<br>
<br>
</span>This is strange for me. I found that Z-matrices are a very bad choic=
e for optimizing rings.<br>
<span class=3D""><br>
&gt; Something along the lines of forcing<br>
&gt; the job to optimize using cartesian coordinates, opt=3D(modredudant,<b=
r>
&gt; cartersian), will not work.<br>
<br>
</span>Are you sure?<br>
<br>
<br>
<br>
<br>
=C2=A0 Sincerely,<br>
=C2=A0 Grigoriy Zhurko.<br>
<span class=3D""><br>
<br>
<br>
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</div></div></blockquote></div><br><br clear=3D"all"><br>-- <br><div class=
=3D"gmail_signature" data-smartmail=3D"gmail_signature"><div dir=3D"ltr"><d=
iv><div dir=3D"ltr"><div><div dir=3D"ltr"><span style=3D"color:rgb(34,34,34=
);font-family:arial;font-size:small;font-style:normal;font-variant:normal;f=
ont-weight:normal;letter-spacing:normal;line-height:normal;text-align:start=
;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;ba=
ckground-color:rgb(255,255,255);display:inline!important;float:none">Franci=
sco Guzman</span><br style=3D"color:rgb(34,34,34);font-family:arial;font-si=
ze:small;font-style:normal;font-variant:normal;font-weight:normal;letter-sp=
acing:normal;line-height:normal;text-align:start;text-indent:0px;text-trans=
form:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,=
255)"><span style=3D"color:rgb(34,34,34);font-family:arial;font-size:small;=
font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:nor=
mal;line-height:normal;text-align:start;text-indent:0px;text-transform:none=
;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);disp=
lay:inline!important;float:none">PhD Candidate</span><div style=3D"color:rg=
b(34,34,34);font-family:arial;font-size:small;font-style:normal;font-varian=
t:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-a=
lign:start;text-indent:0px;text-transform:none;white-space:normal;word-spac=
ing:0px;background-color:rgb(255,255,255)"><span style=3D"background-color:=
rgb(255,255,255)"><font color=3D"#000000"></font></span>Otto H. York Depart=
ment of Chemical, Biological and Pharmaceutical Engineering<br>New Jersey I=
nstitute of Technology</div><div style=3D"color:rgb(34,34,34);font-family:a=
rial;font-size:small;font-style:normal;font-variant:normal;font-weight:norm=
al;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0p=
x;text-transform:none;white-space:normal;word-spacing:0px;background-color:=
rgb(255,255,255)">Email:=C2=A0<font color=3D"#0000ff"><a href=3D"mailto:fg5=
8(a)njit.edu" style=3D"color:rgb(17,85,204)" target=3D"_blank">fg58(a)njit.edu<=
/a>,<span>=C2=A0</span><a href=3D"mailto:guzman.research(a)gmail.com" style=
=3D"color:rgb(17,85,204)" target=3D"_blank">guzman.research(a)gmail.com</a></=
font></div></div></div></div></div></div></div>
</div></div>

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