From owner-chemistry@ccl.net Wed Jun 13 05:12:01 2012
From: "Jean Jules FIFEN julesfifen~~gmail.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: "Quasi free rotors"
Message-Id: <-47076-120613040548-15222-qoS2PKvM62wnXfb7EgR8oQ++server.ccl.net>
X-Original-From: Jean Jules FIFEN <julesfifen]*[gmail.com>
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Date: Wed, 13 Jun 2012 09:05:42 +0100
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Sent to CCL by: Jean Jules FIFEN [julesfifen(!)gmail.com]
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Not integral=grid=*ultraviolet*, but *grid=ultrafine
*
On 12 June 2012 17:17, John Keller jwkeller__alaska.edu <
owner-chemistry:_:ccl.net> wrote:
>
> Sent to CCL by: John Keller [jwkeller---alaska.edu]
> If the methyl group is not directly involved in complex formation,
> just fix a torsion angle using mod redundant. Or, do Opt=tight and
> integral=grid=ultraviolet (if you are using a DFT method).
> John Keller
>
>
> Sent from my iPad
>
> On Jun 12, 2012, at 6:40 AM, "John McKelvey jmmckel~!~gmail.com"
> <owner-chemistry|*|ccl.net> wrote:
>
> >
> > Sent to CCL by: John McKelvey [jmmckel-,-gmail.com]
> > Folks,
> >
> > Hypothetical: Suppose that one has methyl-benzene (toluene) and one
> > can not get the maximum displacement in a geometry optimization to
> > converge due to the "spinning methyl group", but the energy, MAX & RMS
> > gradients and RMS displacement have converged.
> >
> > Now the target is then to do the IR frequencies. I might suppose or
> > hope that in an ideal case that the lowest frequency above the usual
> > first 6, though probably negative, would be this CH3 rotation, and the
> > remainder of the freqs would be real and close to these when the
> > compete optimization might be achieved, would be useful. Too much
> > wishful thinking?
> >
> > The real application is a metal complex with a loosely bound solvent
> > molecule, and the experimental IR spectrum is known, and is otherwise
> > analogous to the above with respect to max displacement. Reasonable
> > to depend upon the computed IR freqs other than the suspect low energy
> > mode?
> >
> > Many thanks!
> >
> > John
> >
> > --
> > John McKelvey
> > 10819 Middleford Pl
> > Ft Wayne, IN 46818
> > 260-489-2160
> > jmmckel : gmail.com>
>
>
--
Jules.
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<div dir=3D"ltr"><font>Not integral=3Dgrid=3D<strong>ultraviolet</strong>, =
but <strong>grid=3Dultrafine=A0<br></strong></font><br>
<div class=3D"gmail_quote">On 12 June 2012 17:17, John Keller <a href=3D"ht=
tp://jwkeller__alaska.edu">jwkeller__alaska.edu</a> <span dir=3D"ltr"><<=
a href=3D"mailto:owner-chemistry:_:ccl.net" target=3D"_blank">owner-chemistry=
:_:ccl.net</a>></span> wrote:<br>
<blockquote style=3D"BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PA=
DDING-LEFT:1ex" class=3D"gmail_quote"><br>Sent to CCL by: John Keller [<a h=
ref=3D"http://jwkeller---alaska.edu/" target=3D"_blank">jwkeller---alaska.e=
du</a>]<br>
If the methyl group is not directly involved in complex formation,<br>just =
fix a torsion angle using mod redundant. Or, do Opt=3Dtight and<br>integral=
=3Dgrid=3Dultraviolet (if you are using a DFT method).<br>John Keller<br><b=
r>
<br>Sent from my iPad<br><br>On Jun 12, 2012, at 6:40 AM, "John McKelv=
ey jmmckel~!~<a href=3D"http://gmail.com/" target=3D"_blank">gmail.com</a>&=
quot;<br><owner-chemistry|*|<a href=3D"http://ccl.net/" target=3D"_blank=
">ccl.net</a>> wrote:<br>
<br>><br>> Sent to CCL by: John McKelvey [jmmckel-,-<a href=3D"http:/=
/gmail.com/" target=3D"_blank">gmail.com</a>]<br>> Folks,<br>><br>>=
; Hypothetical: =A0Suppose that one has methyl-benzene (toluene) and one<br=
>> can not get the maximum displacement in a geometry optimization to<br=
>
> converge due to the "spinning methyl group", but the energy,=
MAX & RMS<br>> gradients and RMS displacement have converged.<br>&g=
t;<br>> Now the target is then to do the IR frequencies. =A0I might supp=
ose or<br>
> hope that in an ideal case that the lowest frequency above the usual<b=
r>> first 6, though probably negative, would be this CH3 rotation, and t=
he<br>> remainder of the freqs would be real and close to these when the=
<br>
> compete optimization might be achieved, would be useful. =A0Too much<b=
r>> wishful thinking?<br>><br>> The real application is a metal co=
mplex with a loosely bound solvent<br>> molecule, and the experimental I=
R spectrum is known, and is otherwise<br>
> analogous to the above with respect to max displacement. =A0Reasonable=
<br>> to depend upon the computed IR freqs other than the suspect low en=
ergy<br>> mode?<br>><br>> Many thanks!<br>><br>> John<br>>=
;<br>
> --<br>> John McKelvey<br>> 10819 Middleford Pl<br>> Ft Wayne,=
IN 46818<br>> <a href=3D"tel:260-489-2160" value=3D"+12604892160">260-4=
89-2160</a><br>> jmmckel : <a href=3D"http://gmail.com/" target=3D"_blan=
k">gmail.com</a>><br>
><br><br><br><br>-=3D This is automatically added to each message by the=
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><br><br></blockquote></div><br><br clear=3D"all"><br>-- <br>
<div dir=3D"ltr"><font size=3D"4"><span style=3D"COLOR:rgb(51,102,255)"><fo=
nt>Jules</font>.</span></font></div><br></div>
--20cf300fb283aa3bcf04c2560c3a--
From owner-chemistry@ccl.net Wed Jun 13 09:25:00 2012
From: "Carles Bo cbo[a]ICIQ.ES" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL:G: SCIPIO: A new tool for scientific computation
Message-Id: <-47077-120611195515-9096-ITTQdtb08NrjJge69yAzrA,+,server.ccl.net>
X-Original-From: Carles Bo <cbo**ICIQ.ES>
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Date: Mon, 11 Jun 2012 23:53:43 +0000
MIME-Version: 1.0
Sent to CCL by: Carles Bo [cbo*|*ICIQ.ES]
SCIPIO: A new tool for scientific computation
The Computational Groups at ICIQ release today SCIPIO (Storing Comprehensibly Interesting Pieces of Inputs and Outputs), a new software platform that solves the problem of storing, managing and processing the most relevant results of computational studies. Current implementation compatible with input and output files from Gaussian, ADF and VASP. Any new file types can be easily added.
Unique features:
� Both command line interface (transparent to Linux bash shell) and Web interface
� Data extractor engine fully independent of database structure and user interfaces
� Almost no recoding is needed for new types of output files
� Molecular substructure searches
� Computing and plotting reaction energy profiles from raw data
� Straightforward generation of Supporting Information PDF or text files
Web site: scipio.iciq.es
Video presentation: http://youtu.be/hMz1_K-s0hg
Video tutorials (English version available soon): http://www.scipio.cat
The Computational Groups -#- ICIQ
(Profs. C. Bo, F. Maseras & N. L�pez)
From owner-chemistry@ccl.net Wed Jun 13 15:35:00 2012
From: "Adebayo A Adeniyi 201205578 * ufh.ac.za" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: Frequency calculation with G03 take too long time without success
Message-Id: <-47078-120613110252-3796-DyiHOilYJtP9O8G4iPIz+Q---server.ccl.net>
X-Original-From: "Adebayo A Adeniyi" <201205578|-|ufh.ac.za>
Date: Wed, 13 Jun 2012 10:23:57 -0400
Sent to CCL by: "Adebayo A Adeniyi" [201205578{}ufh.ac.za]
Dear All,
I am calculating Frequency of some metal-based complexes with external basis set SBKJC VDZ for metal and some selected atoms. The frequency was successful for some but for some it is taking a very long time without any progress and yet the program did not crash. Please what can cause such a very serious delay in frequency calculation that the program did not crash and yet it remains at just one point for many days.
What can I do to make the calculation progress and find the frequency?.
Thanks.
Adebayo Adeniyi
201205578*ufh.ac.za