From owner-chemistry@ccl.net Mon Aug 17 10:03:01 2015 From: "Thomas Exner texner ~ gmx.net" To: CCL Subject: CCL: OpenTox Euro 2015 meeting, 30 Sept - 2 Oct in Dublin Message-Id: <-51589-150817085428-17969-Yjxfoes5uBH5mbqp05xMxg-,-server.ccl.net> X-Original-From: Thomas Exner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 17 Aug 2015 14:54:20 +0200 MIME-Version: 1.0 Sent to CCL by: Thomas Exner [texner . gmx.net] The OpenTox Euro 2015 meeting takes place 30 Sept - 2 Oct in Dublin, Ireland. The conference theme is Reproducible High Quality Safety Science on Complex Systems and will include conference sessions on Information Requirements & Standards, Characterisation of Systems, High Content Screening, Metabolism, Modelling Cellular Perturbations & Responses, Linking Parameters & Evidence across Scales, Simulation, Systems Biology and Knowledge Integration Supporting Decision Making. OpenTox Association Working group meetings will be held on the topics of Application Programming Interfaces, Adverse Outcome Pathways, Data and Metadata Standards and Resource Deployment on the first day of the conference. Persons interested in these working groups but not able to come to the conference please contact Thomas Exner (thomas.exner * douglasconnect.com) for information on how to participate virtually. The meeting will also include a General Assembly of the Association in addition to hands-on modelling and analysis sessions, poster session and knowledge cafes. We are still accepting posters until 31 August. To submit an abstract for the meeting: http://www.opentox.net/submit-abstract-poster-or-chair Information and updates on the program will be posted at: http://www.opentox.net/events/opentox-euro-2015 best regards Barry Hardy President, OpenTox Association On behalf of the Organising Committee On the OpenTox Association Following up on the initial OpenTox project which was funded by the EU under FP7, OpenTox has developed as an open standards platform supporting application and infrastructure development in predictive toxicology and safety assessment. The OpenTox Association was founded 27 March this year as an international member-based non-profit association. The purpose of the Association is to promote the community-based exchange and use of open knowledge, software, methods, tools, data, reference resources, and standards in the scientific activities of predictive toxicology, safety assessment and risk management, including the 3Rs goal of the Reduction, Refinement and Replacement of Animal Testing. More information on the Association: http://www.opentox.net/the-opentox-association From owner-chemistry@ccl.net Mon Aug 17 12:54:00 2015 From: "Dom Esan desan2*o*uic.edu" To: CCL Subject: CCL: Obtaining dipole derivatives wrt x,y,z axes from a freq calc in g09 Message-Id: <-51590-150817124732-17394-bWGleKKGhXoRgQY2yaBbuQ\a/server.ccl.net> X-Original-From: "Dom Esan" Date: Mon, 17 Aug 2015 12:47:30 -0400 Sent to CCL by: "Dom Esan" [desan2{=}uic.edu] Good day all, I was having some issues about how to obtain dipole derivatives with respect to the x, y, and z components of the different normal modes in my molecule from a g09 calculation. However, going through the ccl.net archives, I realized I'd to include iop(7/33=1) with the freq keyword. The issue I'm having now is that including iop(7/33=1) for a opt/freq calculation does not output the dipole derivatives with respect to the x, y, and z components of each mode. Instead, it just gives the intensities for each mode. But, if I run a freq calculation alone, everything is fine (I get the x, y, and z components). My questions: - is there a way I can run the opt/freq job with this iop(7/33=1) included in the route section and get an output which includes the dipole derivatives with respect to the x, y, and z components of the different normal modes? - if I choose to do an opt/freq calculation then run a freq calculation > from the optimized geometry with the iop(7/33=1) option included (so as to get the x, y, and z components of the dipole derivatives), the frequency calculation often fails (convergence failure) or takes even longer to complete than the opt/freq step. What might be wrong here? Thanks for your anticipated assistance. From owner-chemistry@ccl.net Mon Aug 17 14:19:01 2015 From: "Mark Iron Mark.A.Iron]~[weizmann.ac.il" To: CCL Subject: CCL: Obtaining dipole derivatives wrt x,y,z axes from a freq calc in g09 Message-Id: <-51591-150817141658-16123-2enaeFDeVcQsmwQBn/xyuA__server.ccl.net> X-Original-From: Mark Iron Content-Language: en-CA Content-Type: multipart/alternative; boundary="_000_nenseqh4dklrkslugmfbfg701439835385634emailandroidcom_" Date: Mon, 17 Aug 2015 18:16:49 +0000 MIME-Version: 1.0 Sent to CCL by: Mark Iron [Mark.A.Iron[a]weizmann.ac.il] --_000_nenseqh4dklrkslugmfbfg701439835385634emailandroidcom_ Content-Type: text/plain; charset="windows-1255" Content-Transfer-Encoding: quoted-printable For your information, IOps are by design not passed on from the opt step to= the freq. Try running the freq step with the iop from the checkpoint file with geom= =3Dcheckpoint guess=3Dread. This will help with the convergence as the opti= mized wavefunction is used. Hope this helps. Sincerely, Mark. ----------------------------------------------------- Dr. Mark Iron, Computational Chemistry Unit, Department of Chemical Research Support, Kimmelman 252, Weizmann Institute of Science, Rehovot, Israel 76100. Tel: +972 8 934 6218 Fax: +972 8 934 3029 e-mail: mark.a.iron]_[weizmann.ac.il web: http://compchem.weizmann.ac.il/ccu/ No trees were killed in the sending of this message. However, a large number of electrons were terribly inconvenienced. Sent from my Sony Xperia=99 smartphone ---- Dom Esan desan2*o*uic.edu wrote ---- Sent to CCL by: "Dom Esan" [desan2{=3D}uic.edu] Good day all, I was having some issues about how to obtain dipole derivatives with respect to the x, y, and z components of the different normal modes in my molecule from a g09 calculation. However, going through the ccl.net archives, I realized I'd to include iop(7/33=3D1) with the freq keyword. The issue I'm having now is that including iop(7/33=3D1) for a opt/freq calculation does not output the dipole derivatives with respect to the x, y, and z components of each mode. Instead, it just gives the intensities for each mode. But, if I run a freq calculation alone, everything is fine (I get the x, y, and z components). My questions: - is there a way I can run the opt/freq job with this iop(7/33=3D1) included in the route section and get an output which includes the dipole derivatives with respect to the x, y, and z components of the different normal modes? - if I choose to do an opt/freq calculation then run a freq calculation > from the optimized geometry with the iop(7/33=3D1) option included (so as to get the x, y, and z components of the dipole derivatives), the frequency calculation often fails (convergence failure) or takes even longer to complete than the opt/freq step. What might be wrong here? Thanks for your anticipated assistance. -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_nenseqh4dklrkslugmfbfg701439835385634emailandroidcom_ Content-Type: text/html; charset="windows-1255" Content-Transfer-Encoding: quoted-printable

For your information, IOps are by design not passed on from = the opt step to the freq.

Try running the freq step with the iop from the checkpoint f= ile with geom=3Dcheckpoint guess=3Dread. This will help with the convergenc= e as the optimized wavefunction is used.

Hope this helps.

Sincerely,

Mark.

-----------------------------------------------------
Dr. Mark Iron,
Computational Chemistry Unit,
Department of Chemical Research Support,
Kimmelman 252,
Weizmann Institute of Science,
Rehovot, Israel 76100.

Tel: +972 8 934 6218
Fax: +972 8 934 3029

e-mail: m= ark.a.iron]_[weizmann.ac.il
web: http://compchem.we= izmann.ac.il/ccu/

No trees were killed in the sending of this message. However, a large number of electrons were terribly inconvenienced.

Sent from my Sony Xperia=99 smartphone



---- Dom Esan desan2*o*uic.edu wrote ----


Sent to CCL by: "Dom  Esan" [desan2{=3D}uic.edu]
Good day all,

I was having some issues about how to obtain dipole derivatives with
respect to the x, y, and z components of the different normal modes in my <= br> molecule from a g09 calculation. However, going through the ccl.net
archives, I realized I'd to include iop(7/33=3D1) with the freq keyword.
The issue I'm having now is that including iop(7/33=3D1) for a opt/freq calculation does not output the dipole derivatives with respect to the x, <= br> y, and z components of each mode. Instead, it just gives the intensities for each mode. But, if I run a freq calculation alone, everything is fine <= br> (I get the x, y, and z components).

My questions:

- is there a way I can run the opt/freq job with this iop(7/33=3D1)
included in the route section and get an output which includes the dipole <= br> derivatives with respect to the x, y, and z components of the different normal modes?

- if I choose to do an opt/freq calculation then run a freq calculation > from the optimized geometry with the iop(7/33=3D1) option included (so= as
to get the x, y, and z components of the dipole derivatives), the
frequency calculation often fails (convergence failure) or takes even
longer to complete than the opt/freq step. What might be wrong here?

Thanks for your anticipated assistance.



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