From owner-chemistry@ccl.net Tue Sep 23 08:19:00 2014 From: "Henrique Junior henriquecsj[]gmail.com" To: CCL Subject: CCL:G: MOPAC - Problem with Iron complex and gradients Message-Id: <-50524-140923081542-3812-No4elLgUDRgLzjLKqbqcbg]_[server.ccl.net> X-Original-From: Henrique Junior Content-Type: multipart/alternative; boundary=089e0149c0b006131d0503ba860a Date: Tue, 23 Sep 2014 09:14:50 -0300 MIME-Version: 1.0 Sent to CCL by: Henrique Junior [henriquecsj|gmail.com] --089e0149c0b006131d0503ba860a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi, I'm very sorry for my delay (I was having connection issues). I'll give it a try and share my results. Thank you. 2014-09-17 10:26 GMT-03:00 Henrique Castro Silva Junior henriquecsj|,| gmail.com : > > Sent to CCL by: "Henrique Castro Silva Junior" [henriquecsj**gmail.com] > Hi, I am an undergraduate in Chemistry from Brazil, writing my thesis as > a requirement to receive my graduation. Im working in thermodynamic (and > MO) descriptions that takes place in [Fe(OH2)6]2+ --> [Fe(OH2)6]3+, > mostly using computational chemistry softwares. > I have decided to use MOPAC2012 and Gabedit (as a GUI), but Im having > problems in getting realistic values. Here is my input: > > * =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D > * Input file for Mopac > * =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D > PM7 THERMO ROT=3D1 EPS=3D78.39 RSOLV=3D1.3 UHF CHARGE=3D2 Quintet BONDS= AUX > Mopac file generated by Gabedit > Fe -0.1136 1 -0.9091 1 0.0000 1 > O -0.1136 1 0.9109 1 0.0000 1 > H 0.5055 1 1.2122 1 -0.7127 1 > O 1.7064 1 -0.9091 1 0.0000 1 > H 2.0628 1 -1.3124 1 0.8307 1 > O -0.1136 1 -0.9091 1 -1.8200 1 > H -0.4817 1 -1.7682 1 -2.1477 1 > O -0.1136 1 -2.7291 1 0.0000 1 > H -0.8413 1 -3.0457 1 0.5936 1 > O -1.9336 1 -0.9091 1 0.0000 1 > H -2.2569 1 -1.5900 1 -0.6429 1 > O -0.1136 1 -0.9091 1 1.8200 1 > H -1.0440 1 -0.9414 1 2.1566 1 > H -2.2613 1 -0.0487 1 -0.3649 1 > H 0.7122 1 -3.0886 1 0.4108 1 > H -0.7542 1 -0.2257 1 -2.1427 1 > H 2.0192 1 -1.5032 1 -0.7289 1 > H 0.3089 1 -1.7285 1 2.1807 1 > H 0.3233 1 1.2180 1 0.8341 1 > > The result is this: > > GRADIENT NORM =3D 298.62520 > ** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED, > (LIMIT=3D10) ** > EITHER ADD 'LET' OR REDUCE GRADIENT > USING 'TS' OR OTHER GEOMETRY OPTIMIZER > > If I add the keyword LET the calculation goes on, returning this: > HEAT OF FORMATION =3D -39.019942 KCALS/MOLE > > With bond distance of ~1,82 A (much less than what is expected, right?). > Then, I tried to perform an optimization first, to reduce the gradient > and do not use LET: > PM7 XYZ EPS=3D78.39 RSOLV=3D1.3 UHF CHARGE=3D2 Quintet BONDS AUX > > The result is a fragmentation, [Fe(OH)6] + 6H and the same result (the > fragmentation) goes with Gaussian09. > Any help will be very much appreciated and Im sorry if Im making some > obvious and stupid mistake here, but most of my knowledge on > computational chemistry Ive learned by myself. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 *Henrique C. S. Junior* Qu=C3=ADmica Industrial - UFRRJ Centro de Processamento de Dados - PMP --089e0149c0b006131d0503ba860a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi, I'm very sorry for my delay (I was having connecti= on issues).
I'll give it a try and share my results.

=
Thank you.

2014-09-17 10:26 GMT-03:00 Henrique Castro Silva Junior he= nriquecsj|,|gmail.com &l= t;owner-chemis= try#ccl.net>:

Sent to CCL by: "Henrique Castro Silva Junior" [henriquecsj**gmail.com]
Hi, I am an undergraduate in Chemistry from Brazil, writing my thesis as a requirement to receive my graduation. Im working in thermodynamic (and MO) descriptions that takes place in [Fe(OH2)6]2+ --> [Fe(OH2)6]3+,
mostly using computational chemistry softwares.
I have decided to use MOPAC2012 and Gabedit (as a GUI), but Im having
problems in getting realistic values. Here is my input:

* =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D
* Input file for Mopac
* =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D
PM7 THERMO ROT=3D1=C2=A0 EPS=3D78.39 RSOLV=3D1.3 UHF CHARGE=3D2 Quintet=C2= =A0 BONDS AUX
Mopac file generated by Gabedit
Fe=C2=A0 -0.1136=C2=A0 1 -0.9091=C2=A0 1 0.0000=C2=A0 1
O=C2=A0 -0.1136=C2=A0 1 0.9109=C2=A0 1 0.0000=C2=A0 1
H=C2=A0 0.5055=C2=A0 1 1.2122=C2=A0 1 -0.7127=C2=A0 1
O=C2=A0 1.7064=C2=A0 1 -0.9091=C2=A0 1 0.0000=C2=A0 1
H=C2=A0 2.0628=C2=A0 1 -1.3124=C2=A0 1 0.8307=C2=A0 1
O=C2=A0 -0.1136=C2=A0 1 -0.9091=C2=A0 1 -1.8200=C2=A0 1
H=C2=A0 -0.4817=C2=A0 1 -1.7682=C2=A0 1 -2.1477=C2=A0 1
O=C2=A0 -0.1136=C2=A0 1 -2.7291=C2=A0 1 0.0000=C2=A0 1
H=C2=A0 -0.8413=C2=A0 1 -3.0457=C2=A0 1 0.5936=C2=A0 1
O=C2=A0 -1.9336=C2=A0 1 -0.9091=C2=A0 1 0.0000=C2=A0 1
H=C2=A0 -2.2569=C2=A0 1 -1.5900=C2=A0 1 -0.6429=C2=A0 1
O=C2=A0 -0.1136=C2=A0 1 -0.9091=C2=A0 1 1.8200=C2=A0 1
H=C2=A0 -1.0440=C2=A0 1 -0.9414=C2=A0 1 2.1566=C2=A0 1
H=C2=A0 -2.2613=C2=A0 1 -0.0487=C2=A0 1 -0.3649=C2=A0 1
H=C2=A0 0.7122=C2=A0 1 -3.0886=C2=A0 1 0.4108=C2=A0 1
H=C2=A0 -0.7542=C2=A0 1 -0.2257=C2=A0 1 -2.1427=C2=A0 1
H=C2=A0 2.0192=C2=A0 1 -1.5032=C2=A0 1 -0.7289=C2=A0 1
H=C2=A0 0.3089=C2=A0 1 -1.7285=C2=A0 1 2.1807=C2=A0 1
H=C2=A0 0.3233=C2=A0 1 1.2180=C2=A0 1 0.8341=C2=A0 1

The result is this:

GRADIENT NORM =3D 298.62520
=C2=A0** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED,
(LIMIT=3D10) **
=C2=A0EITHER ADD 'LET' OR REDUCE GRADIENT
=C2=A0USING 'TS' OR OTHER GEOMETRY OPTIMIZER

If I add the keyword LET the calculation goes on, returning this:
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 HEAT OF FORMATION =3D=C2=A0 =C2=A0 =C2= =A0-39.019942 KCALS/MOLE

With bond distance of ~1,82 A (much less than what is expected, right?). Then, I tried to perform an optimization first, to reduce the gradient
and do not use LET:
PM7 XYZ=C2=A0 EPS=3D78.39 RSOLV=3D1.3 UHF CHARGE=3D2 Quintet=C2=A0 BONDS AU= X

The result is a fragmentation, [Fe(OH)6] + 6H and the same result (the
fragmentation) goes with Gaussian09.
Any help will be very much appreciated and Im sorry if Im making some
obvious and stupid mistake here, but most of my knowledge on
computational chemistry Ive learned by myself.



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--
Henr= ique C. S. Junior
Qu=C3=ADmica Industrial - UFRRJ
Centro d= e Processamento de Dados - PMP
--089e0149c0b006131d0503ba860a-- From owner-chemistry@ccl.net Tue Sep 23 14:57:00 2014 From: "Matthew Kirkby Matthew.Kirkby/a\zingconferences.com" To: CCL Subject: CCL: 2nd Mathematical and Computational Medicine Conference Message-Id: <-50525-140923111145-13184-ulm9QKr0DAmt/onxWVyslQ*server.ccl.net> X-Original-From: "Matthew Kirkby" Date: Tue, 23 Sep 2014 11:11:37 -0400 Sent to CCL by: "Matthew Kirkby" [Matthew.Kirkby!^!zingconferences.com] Dear CCL Subscriber, I am writing to let you know of a conference which may be of interest to your current research. The 2nd Zing Mathematical and Computational Chemistry Conference will be taking place at the Omni Hotel in Cancun, > from 1st - 4th December 2014. See below the synopsis, written by conference chair, Andrzej Kloczkowski: "The purpose of the 2nd Zing Conference on Mathematical and Computational Medicine is to bring together eminent scholars with expertise in various fields of mathematical and computational medicine, as well as experimentalists and medical doctors interested in application of computational methods in clinical studies. The mathematical and computational medicine is now one of the most important and rapidly growing fields of modern medicine, and will become even more important in near future, when the cost of individual human gene sequencing becomes affordable for mass-scale clinical use (The $1000 Human Genome). New sequencing techniques, such as RNA-Seq produce enormous amount of information on the transcriptome in healthy and diseased cells, that need a development of new mathematical and computational methods to extract the most important medical information. The scope of the proposed Zing Conference will cover many different fields mathematical and computational medicine and biomedical informatics, such as genetics, genomics, epigenetics, and epigenomics of various diseases including mental and learning disorders, autism, and somatic diseases, with a special emphasis on cancer, protein misfolding disorders related to amyloid formation in neurogenerative diseases (such as Alzheimers and Parkinsons disease), gene regulation, biomarker development, computer aided drug development, computational pharmacodynamics, computational immunology, systems biology and its extension to systems medicine, machine learning methods in application to biomedical data, applicability of computational methods in personalized medicine, and regenerative medicine." We hope many of you will be able to join us in Cancun for the unique and exciting conference. Best regards, Matthew Kirkby matthew.kirkby:_:zingconferences.com From owner-chemistry@ccl.net Tue Sep 23 15:32:00 2014 From: "Fedor Goumans goumans*|*scm.com" To: CCL Subject: CCL: ADF modeling suite 2014 released Message-Id: <-50526-140923114844-16882-pO9F6Lq7aPrkLhLhY2LoDg ~ server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 23 Sep 2014 17:48:19 +0200 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans++scm.com] Dear Computational Chemists, We are happy to announce the 2014 release of the ADF modeling suite, and encourage you to try it out with a 30-day free evaluation: http://www.scm.com/trial The excellent graphical interface integrated with our computational engines from DFT to MD facilitates the study of tough problems in chemistry and materials science: from analyzing bonding and spectroscopic properties in heavy elements and transition metal compounds, to modeling nanoparticles, crystals, and large complex reaction mixtures. The ADF modeling suite consists of our GUI, the powerful DFT codes ADF (molecules) and BAND (surfaces, bulk), the semi-empirical DFTB and MOPAC2012 modules, ReaxFF, and COSMO-RS. The binaries for the entire suite work out of the box, in parallel, on all popular platforms (Windows, Mac, Linux). A summary of new features and improvements in the 2014 release: - lower-memory, better parallel SCF in ADF - significant speed-ups in DFTB and the periodic DFT code BAND (AO-based) - many-body dispersion functionals (Tkatchenko et al.) - conformer search, support for multiple configurations, spectra averaging - TD-DFTB and DFTB-NEGF, with electronic parameters for 87 elements - ReaxFF force field optimizer, Grand Canonical Monte Carlo - COSMO-SAC 2013-ADF parameters For a complete list and more detailed description, see: http://www.scm.com/Doc/Doc2014/Background/Updates/page1.html We are particularly grateful to all our past and present ADF developers: http://www.scm.com/About/AboutAuthors.html With kind regards, on behalf of the SCM team, Fedor Goumans -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans(-)scm.com http://www.scm.com