From owner-chemistry@ccl.net Wed Aug 5 09:21:00 2009 From: "Amin Ordikhani a.ordikhani:_:gmail.com" To: CCL Subject: CCL:G: NMR with Gaussian Message-Id: <-39926-090805091735-32499-C8g0CzEvj1la+nnHCuT/uQ : server.ccl.net> X-Original-From: "Amin Ordikhani" Date: Wed, 5 Aug 2009 09:17:31 -0400 Sent to CCL by: "Amin Ordikhani" [a.ordikhani^gmail.com] Dear CCLers, I'm trying to do a NMR-Gaussian job on ionic liquids. I used "All NMR methods". Although IGAIM and CSGT were better than CIAO method, but still the spectra has a lot differences with the real one. # nmr=all rb3lyp/3-21g geom=connectivity The sample is pure, I mean there is no solvent, just some impurities of water (0.5%) Now I'm wondering 1- how I can apply the solution situation using gaussian parameters? 2- how can I apply the effect of other molecules? Are these possible at all???? Thanks in advance, Amin From owner-chemistry@ccl.net Wed Aug 5 10:31:01 2009 From: "Eduardo Lemos de Sa edulsa*o*quimica.ufpr.br" To: CCL Subject: CCL: How to calculate a bond energy Message-Id: <-39927-090805085322-29829-QC0C/v7tn3S2AwXa3ct9Jw!=!server.ccl.net> X-Original-From: "Eduardo Lemos de Sa" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 5 Aug 2009 09:23:09 -0300 (BRT) MIME-Version: 1.0 Sent to CCL by: "Eduardo Lemos de Sa" [edulsa#%#quimica.ufpr.br] Sirs and Ladies I have a silly questions: how can I calculate a energy rising from a bond between two atoms in a organic molecule? I guess that the answer can be: calculate the SCF energy for the whole molecule, for two radicals originated from the dissociation. Thus, bound energy would be: sum (SCF energy for radicals) - SCF energy for the complete molecule. Am I right? Thank you in advance Yours Eduardo -- Eduardo Lemos de Sa edulsa]~[quimica.ufpr.br Professor Assoc. II - Departamento de Quimica Universidade Federal do Parana C. P. 19081 81531-990 Curitiba/PR - Brazil Fone (41) 3361 3300 From owner-chemistry@ccl.net Wed Aug 5 12:03:01 2009 From: "Hoa Nguyen hoa_giao_nguyen[a]yahoo.com" To: CCL Subject: CCL:G: Gaussian's Hessian matrix Message-Id: <-39928-090805024315-29584-DgO5EvwhqLcQx0gI6Pa8xw*server.ccl.net> X-Original-From: Hoa Nguyen Content-Type: multipart/alternative; boundary="0-1333244192-1249451267=:31126" Date: Tue, 4 Aug 2009 22:47:47 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Hoa Nguyen [hoa_giao_nguyen|,|yahoo.com] --0-1333244192-1249451267=:31126 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Does anyone know the unit of the Hessian Matrix in the check point file of = a Gaussian calculation (it is called=A0Cartesian Force Constants)?=A0 I think it must be Hartree/Angstrom^2. However when I diagonalized the matr= ix to obtain vibrational frequency (I follow the paper "Vibrational Analysi= s in Gaussian" from Dr Ochterski), I cannot get the same frequencies like t= he Gaussian results. Thanks, Hoa Nguyen --- On Sat, 10/4/08, Gennady L Gutsev gennady.gutsev_+_famu.edu wrote: > From: Gennady L Gutsev gennady.gutsev_+_famu.edu Subject: CCL:G: G03 on Barcelona's To: "Nguyen, Hoa G " Date: Saturday, October 4, 2008, 8:39 PM Sent to CCL by: "Gennady L Gutsev" [gennady.gutsev/a\famu.edu] Hi everybody, we have installed a cluster of 50 Barcelona's but Gaussian jobs=20 are not running. If I submit, say, 10 jobs, 5 die in a few seconds, 2 in a few minutes, 3 in hours to several days. =A0=A0=A0Have anybody experienced similar problems? I wonder what could be wrong: or processors themselves, either G03 is not well adapted to the Barcelona platform, either the problem with the system support?=20 =A0=A0=A0The company we purchased the cluster from is Western Scientific (C= A). Can anybody say a good word about this company? =A0 =A0 Thank you all. Gennady -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig=A0 (login: ccl, Password: search)=A0 =A0 =A0=0A=0A=0A --0-1333244192-1249451267=:31126 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,

Does anyone know the u= nit of the Hessian Matrix in the check point file of a Gaussian calculation= (it is called Cartesian Force Constants)? 

<= div>I think it must be Hartree/Angstrom^2. However when I diagonalized the = matrix to obtain vibrational frequency (I follow the paper "Vibrational Ana= lysis in Gaussian" from Dr Ochterski), I cannot get the same frequencies li= ke the Gaussian results.

Thanks,

Hoa Nguyen

--- On Sat, 10/4/08, Gennady L Gutsev g= ennady.gutsev_+_famu.edu <owner-chemistry+/-ccl.net> wrote:<= br>

From: Gennady L Gutsev gennady.gutsev_+_fam= u.edu <owner-chemistry+/-ccl.net>
Subject: CCL:G: G03 on Barcelona's
To: "Nguyen, Hoa G " <hoa_giao_nguyen+/-yahoo.com&= gt;
Date: Saturday, October 4, 2008, 8:39 PM


Sent to CCL by: "Gennady L Gutsev" [gennady.gutsev/a\famu.edu]
=
Hi everybody,

we have installed a cluster of 50 Barcelona's but = Gaussian jobs
are not running. If I submit, say, 10 jobs, 5 die in a fe= w seconds,
2 in a few minutes, 3 in hours to several days.
 &nbs= p; Have anybody experienced similar problems? I wonder what could bewrong: or processors themselves, either G03 is not well adapted to
the= Barcelona platform, either the problem with the system support?
 =   The company we purchased the cluster from is Western Scientific= (CA).
Can anybody say a good word about this company?
    = Thank you all.
Gennady



-=3D This is automatically added t= o each message by the mailing script =3D-the strange characters on t= he top line to the +/- sign. You can also
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<= br>=0A=0A --0-1333244192-1249451267=:31126-- From owner-chemistry@ccl.net Wed Aug 5 13:30:01 2009 From: "may abdelghani may01dz ~ yahoo.fr" To: CCL Subject: CCL: energies of chemical bonds Message-Id: <-39929-090805055236-30302-Tstdanudpsw4nN3dfAn4kw|,|server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-1446436994-1249462343=:77401" Date: Wed, 5 Aug 2009 08:52:23 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz- -yahoo.fr] --0-1446436994-1249462343=:77401 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear CCL's=0A=0AHow I can calculate the energies of chemical bonds,=0Ain AD= F=0A=0Athank you very much,=0A=0A=0A=0A --0-1446436994-1249462343=:77401 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

Dear CCL's

= =0A=0A

How I can calculate the energies of chemical bonds,=0Ain ADF

=0A=0A

thank you very much,

=0A
=0A=0A=0A=0A --0-1446436994-1249462343=:77401-- From owner-chemistry@ccl.net Wed Aug 5 14:29:01 2009 From: "Vincent Leroux vincent.leroux!=!loria.fr" To: CCL Subject: CCL: A code to evaluate the quality of molecular structure Message-Id: <-39930-090805142553-30777-02uYUYMEdxl9IV8LaaCfyw-#-server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 05 Aug 2009 20:25:41 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux . loria.fr] Hi Shahar, You can use Szybki for evaluating quickly the internal energy of your conformations (so the unrealistically distorted ones will be spotted easily), and if this is needed, minimize them. http://www.eyesopen.com/products/applications/szybki.html This is commercial software, so you will not get the code, but this is free for academics, and you can have access to the OpenEye APIs. In addition, for generating sensible rotamer sets, you can also try Omega. VL Shahar Keinan skeinan^gmail.com a écrit : > Sent to CCL by: "Shahar Keinan" [skeinan _ gmail.com] > Hi CCLers, > > I am looking for a code that will be able to evaluate whether or not the geometry I got from a calculation is a reasonable one. > For example, if the carbon-carbon bond is longer then 3.0A, probably the molecule broke down. > > I am optimizing the geometry a large number of molecules, with several rotamers per molecule. Some of the rotamers have a considerable amount of strain, and thus fall apart. I have too many molecules to be able to look at each structure. > > Any help is greatly appreciated, > Shahar Keinan > > > From owner-chemistry@ccl.net Wed Aug 5 19:53:00 2009 From: "Rommel B Viana rommelbv^-^yahoo.com.br" To: CCL Subject: CCL: ORCA - error termination in ORCA_GTOInt Message-Id: <-39931-090805194034-14575-atTEh51E+jvLlrTmx1LfZg/a\server.ccl.net> X-Original-From: "Rommel B Viana" Date: Wed, 5 Aug 2009 19:40:30 -0400 Sent to CCL by: "Rommel B Viana" [rommelbv+*+yahoo.com.br] Dear CCL I performed a calculation and find an error. I am runing the calculation in the same directory of the executables, to make sure that programs can call each other.Could anyone suggest a way out, or point me to my error? Thanks, Rommel B. Viana ================================================================================ INPUT FILE ================================================================================ NAME = co.inp | 1> # | 2> # | 3> # | 4> %method method HF | 5> ProgSCF "orca_scf.exe" | 6> ProgGTOInt "orca_gtoint.exe" | 7> end | 8> ! noautostart | 9> %basis basis SV | 10> end | 11> * xyz 0 1 | 12> C 0 0 0 | 13> O 0 0 1.13 | 14> * | 15> | 16> ****END OF INPUT**** ================================================================================ **************************** * Single Point Calculation * **************************** --------------------------------- CARTESIAN COORDINATES (ANGSTROEM) --------------------------------- C 0.000000 0.000000 0.000000 O 0.000000 0.000000 1.130000 ---------------------------- CARTESIAN COORDINATES (A.U.) ---------------------------- NO LB ZA FRAG MASS X Y Z 0 C 6.0000 0 12.011 0.000000 0.000000 0.000000 1 O 8.0000 0 15.999 0.000000 0.000000 2.135391 -------------------------------- INTERNAL COORDINATES (ANGSTROEM) -------------------------------- C 0 0 0 0.000000 0.000 0.000 O 1 0 0 1.130000 0.000 0.000 --------------------------- INTERNAL COORDINATES (A.U.) --------------------------- C 0 0 0 0.000000 0.000 0.000 O 1 0 0 2.135391 0.000 0.000 --------------------- BASIS SET INFORMATION --------------------- There are 2 groups of distinct atoms Group 1 Type C : 7s4p contracted to 3s2p pattern {511/31} Group 2 Type O : 7s4p contracted to 3s2p pattern {511/31} Atom 0C basis set group => 1 Atom 1O basis set group => 2 sh: orca_gtoint.exe: command not found ORCA finished by error termination in ORCA_GTOInt ORCA finished by error termination in ORCA_GTOInt