From owner-chemistry@ccl.net Tue Oct 28 01:20:01 2014 From: "Ramesh Kumar rameshchitumalla:-:gmail.com" To: CCL Subject: CCL:G: Problem with the convergence of Maximium and RMS displacement Message-Id: <-50648-141028011730-6222-hu6BHzHogYtQLFK7sMR7hg[-]server.ccl.net> X-Original-From: Ramesh Kumar Content-Type: multipart/alternative; boundary=f46d0418283c15d14f050674c378 Date: Tue, 28 Oct 2014 14:17:22 +0900 MIME-Version: 1.0 Sent to CCL by: Ramesh Kumar [rameshchitumalla[-]gmail.com] --f46d0418283c15d14f050674c378 Content-Type: text/plain; charset=UTF-8 Dear Radhika, There are many reasons caused by this error. It means that the Gaussian job terminated abnormally and the geometry optimization has not converged. You can (may) fix the error by doing the following any one or all, > Try increasing the value by specifying OPT=(MaxCycle=N) > If your initial starting structure is not good, then take the structure > from optimized at a lower level of theory (HF in your case). > You can use opt=CalcFC option > If these methods fail, another option would be to change the optimization method from the default to another type, such as opt=ef or opt=gdiis Hope it helps On Tue, Oct 28, 2014 at 12:39 PM, Radhika Narayanan radhika.narayanan.n|*| gmail.com wrote: > > Sent to CCL by: "Radhika Narayanan" [radhika.narayanan.n- -gmail.com] > Dear all, > > I am dealing with the IR spectra of organometallic compounds.While doing > the optimization using DFT functional, I encounter the following trouble: > > Maximum Force 0.000079 0.000450 YES > RMS Force 0.000018 0.000300 YES > Maximum Displacement 0.116059 0.001800 NO > RMS Displacement 0.028645 0.001200 NO > > Error termination request processed by link 9999. > > However, optimization at HF level using the same basis set gave a > converged geometry. > > Maximum Force 0.000004 0.000450 YES > RMS Force 0.000001 0.000300 YES > Maximum Displacement 0.001674 0.001800 YES > RMS Displacement 0.000428 0.001200 YES > > What might be the reason for this error?Could anyone suggest a solution > for this problem? > > Thanks in advance, > sincerely, > Radhika> > > -- *With Best Regards* *Dr. CH. Ramesh Kumar* Post Doctoral Research Fellow Cyclotron Research Centre, Pusan National University, Busan. Republic of Korea, 609735 --f46d0418283c15d14f050674c378 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Radhika,

There are many reasons caused by this err= or. It means that the Gaussian job terminated abnormally and the geometry o= ptimization has not converged.

You can (may) fix the error by doing the follo= wing any one or all,

> Try increasing the value by specifying OPT=3D(MaxCy= cle=3DN)

> If your initial starting structure is not good, then take = the structure from optimized at a lower level of theory (HF in your case).<= /font>

&g= t; You can use opt=3DCalcFC option

> If these methods fail, another optio= n would be to change the optimization method from the default to another ty= pe,=C2=A0
such as=C2=A0
opt=3Def =C2=A0or=C2=A0
= opt=3Dgdiis

Hope it helps

On Tue, Oct 28, 2014 at 12:39 PM, Radhika = Narayanan radhika.narayanan.n|*|gmail.com = <owner-chemistry _ ccl.net> wrote:

Sent to CCL by: "Radhika=C2=A0 Narayanan" [radhika.narayanan.n- -= gmail.com]
Dear all,

I am dealing with the IR spectra of organometallic compounds.While doing the optimization using DFT functional, I encounter the following trouble:
=C2=A0Maximum Force=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.000079=C2=A0= =C2=A0 =C2=A00.000450=C2=A0 =C2=A0 =C2=A0YES
=C2=A0RMS=C2=A0 =C2=A0 =C2=A0Force=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 0.000018=C2=A0 =C2=A0 =C2=A00.000300=C2=A0 =C2=A0 =C2=A0YES
=C2=A0Maximum Displacement=C2=A0 =C2=A0 =C2=A00.116059=C2=A0 =C2=A0 =C2=A00= .001800=C2=A0 =C2=A0 =C2=A0NO
=C2=A0RMS=C2=A0 =C2=A0 =C2=A0Displacement=C2=A0 =C2=A0 =C2=A00.028645=C2=A0= =C2=A0 =C2=A00.001200=C2=A0 =C2=A0 =C2=A0NO

Error termination request processed by link 9999.

However, optimization at HF level using the same basis set gave a
converged geometry.

=C2=A0Maximum Force=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.000004=C2=A0= =C2=A0 =C2=A00.000450=C2=A0 =C2=A0 =C2=A0YES
=C2=A0RMS=C2=A0 =C2=A0 =C2=A0Force=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 0.000001=C2=A0 =C2=A0 =C2=A00.000300=C2=A0 =C2=A0 =C2=A0YES
=C2=A0Maximum Displacement=C2=A0 =C2=A0 =C2=A00.001674=C2=A0 =C2=A0 =C2=A00= .001800=C2=A0 =C2=A0 =C2=A0YES
=C2=A0RMS=C2=A0 =C2=A0 =C2=A0Displacement=C2=A0 =C2=A0 =C2=A00.000428=C2=A0= =C2=A0 =C2=A00.001200=C2=A0 =C2=A0 =C2=A0YES

What might be the reason for this error?Could anyone suggest a solution
for this problem?

Thanks in advance,
sincerely,
Radhika



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--

With Best Regards<= /span>

Dr. CH. Ramesh Kumar
Post Doctoral Resear= ch Fellow
Cyclotron Research Centre,
Pusan = National University, Busan.
Republic of Korea, 609735


--f46d0418283c15d14f050674c378-- From owner-chemistry@ccl.net Tue Oct 28 01:54:01 2014 From: "Robert Molt r.molt.chemical.physics[*]gmail.com" To: CCL Subject: CCL:G: Problem with the convergence of Maximium and RMS displacement Message-Id: <-50649-141028014132-16495-EHx8c9ZAyfg25MWMbwzFkg(0)server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 28 Oct 2014 01:41:24 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics||gmail.com] An "optimized" geometry can be judged by different criteria. You're using Gaussian, which uses the "Displacement" criteria. Other softwares do not, as they judge it to be irrelevant (it judges whether the value of the geometric parameter is changing much; if the parameter changes a lot, and the forces don't change, you have a floppy molecule...maybe you have very soft dihedral potentials). I personally do not regard the displacement as a meaningful criteria for an optimized structure, and nor do the ACES and GAMESS softwares (just force and RMS force). On 10/27/14 11:39 PM, Radhika Narayanan radhika.narayanan.n|*|gmail.com wrote: > Sent to CCL by: "Radhika Narayanan" [radhika.narayanan.n- -gmail.com] > Dear all, > > I am dealing with the IR spectra of organometallic compounds.While doing > the optimization using DFT functional, I encounter the following trouble: > > Maximum Force 0.000079 0.000450 YES > RMS Force 0.000018 0.000300 YES > Maximum Displacement 0.116059 0.001800 NO > RMS Displacement 0.028645 0.001200 NO > > Error termination request processed by link 9999. > > However, optimization at HF level using the same basis set gave a > converged geometry. > > Maximum Force 0.000004 0.000450 YES > RMS Force 0.000001 0.000300 YES > Maximum Displacement 0.001674 0.001800 YES > RMS Displacement 0.000428 0.001200 YES > > What might be the reason for this error?Could anyone suggest a solution > for this problem? > > Thanks in advance, > sincerely, > Radhika> > From owner-chemistry@ccl.net Tue Oct 28 03:41:01 2014 From: "Mariusz Radon mariusz.radon/a\gmail.com" To: CCL Subject: CCL: Problem with the convergence of Maximium and RMS displacement Message-Id: <-50650-141028034018-6116-zReZYwU0ZOL7RNCARVBwLw**server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 28 Oct 2014 08:40:11 +0100 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon_+_gmail.com] On 10/28/2014 04:39 AM, Radhika Narayanan radhika.narayanan.n|*|gmail.com wrote: > Sent to CCL by: "Radhika Narayanan" [radhika.narayanan.n- -gmail.com] > Dear all, > > I am dealing with the IR spectra of organometallic compounds.While doing > the optimization using DFT functional, I encounter the following trouble: > > Maximum Force 0.000079 0.000450 YES > RMS Force 0.000018 0.000300 YES > Maximum Displacement 0.116059 0.001800 NO > RMS Displacement 0.028645 0.001200 NO > > Error termination request processed by link 9999. > > However, optimization at HF level using the same basis set gave a > converged geometry. > > Maximum Force 0.000004 0.000450 YES > RMS Force 0.000001 0.000300 YES > Maximum Displacement 0.001674 0.001800 YES > RMS Displacement 0.000428 0.001200 YES > > What might be the reason for this error?Could anyone suggest a solution > for this problem? > Dear Radhika, Have you tried to increase the number of steps in geometry optimization procedure? E.g., Opt(MaxCycles=300). Take care, Mariusz> > -- Dr Mariusz Radon, Ph.D. Coordination Chemistry Group Faculty of Chemistry Jagiellonian University ul. Ingardena 3, 30-060 Krakow, Poland http://www2.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Tue Oct 28 07:19:00 2014 From: "Prof Ponnadurai Ramasami ramchemi(a)intnet.mu" To: CCL Subject: CCL: Call for Paper-9th Workshop on Computational Chemistry and Its Applications-Part of ICCS 2015 Message-Id: <-50651-141028022206-4029-C3FziTqo1U+7nPBTpmCRXg*_*server.ccl.net> X-Original-From: "Prof Ponnadurai Ramasami" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0027_01CFF299.003512B0" Date: Tue, 28 Oct 2014 10:21:50 +0400 MIME-Version: 1.0 Sent to CCL by: "Prof Ponnadurai Ramasami" [ramchemi:intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_0027_01CFF299.003512B0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear Sir/Madam, The 9th Workshop on Computational Chemistry and Its Applications (9th = CCA) will be organised as part of the International Conference on = Computational Science (ICCS 2015). ICCS 2015 will be held from 1st to 3rd June 2015 in Reykjavik, Iceland. http://www.iccs-meeting.org/iccs2015/=20 You are invited to submit full paper/s to be considered for the 9th CCA = workshop.=20 Prof Hannes J=C3=B3nsson = > from the University of Iceland will deliver the keynote address entitled = "Calculations of molecules and solids using self-interaction corrected = energy functionals and unitary optimization of complex orbitals". All details are available on the workshop webpage, = http://sites.uom.ac.mu/cca/ All papers will be peer-reviewed and accepted papers (oral or poster) = will be published in Procedia Computer Science ( = = http://www.elsevier.com/wps/find/journaldescription.cws_home/719435/descr= iption) Let me know if you need any more information.=20 Looking forward to receive your full paper/s. Kind regards, Prof Ponnadurai Ramasami=20 9th CCA Workshop Organiser Professor Ponnadurai Ramasami | FRSC, FICCE, CSci, CChem | Computational = Chemistry Group, Department of Chemistry, Faculty of Science, University = of Mauritius, R=C3=A9duit, Mauritius | Tel: +230 403-7507 | Fax: +230 = 465-6928 | | ramchemi(!)intnet.mu | = www.uom.ac.mu | http://sites.uom.ac.mu/ccuom/ | < Chemistry I Computational I Chemistry > =3D Useful results < Chemistry = I Chemistry > =C3=BC Please think about the environment. Print this email only if = required. =20 P Think green. Think before you print. =20 =20 =20 ------=_NextPart_000_0027_01CFF299.003512B0 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable

Dear Sir/Madam,

The 9th Workshop on Computational Chemistry = and Its Applications (9th CCA) will be organised as part of = the International Conference on Computational Science (ICCS = 2015).

ICCS 2015 will be held from 1st to = 3rd June 2015 in Reykjavik, Iceland.

http://www.iccs-meeting.or= g/iccs2015/

You are invited to submit full paper/s to be = considered for the 9th CCA workshop.

Prof Hannes J=C3=B3nsson from the University of Iceland will deliver = the keynote address entitled "Calculations of molecules and solids = using self-interaction corrected energy functionals and unitary = optimization of complex orbitals".

All details are available on the workshop = webpage, http://sites.uom.ac.mu/cca/

All papers will be peer-reviewed and accepted = papers (oral or poster) will be published in Procedia Computer Science = (http://www.elsevier.com/wps/find/journaldescripti= on.cws_home/719435/description)

Let me know if you need any more information. =

Looking forward to receive your full = paper/s.

Kind regards,

Prof Ponnadurai Ramasami =

9th CCA Workshop = Organiser

Professor Ponnadurai Ramasami | FRSC, FICCE, CSci, CChem | = Computational Chemistry Group, Department of Chemistry, Faculty of = Science, University of Mauritius, R=C3=A9duit, Mauritius | Tel: +230 = 403-7507 | Fax: +230 465-6928 = | |  ramchemi(!)intnet.mu | www.uom.ac.mu | http://sites.uom.ac.mu/ccuom/ = |

<= ; Chemistry I Computational I Chemistry > =3D Useful results < = Chemistry I Chemistry >

=C3=BC Please = think about the environment. Print this email only if required.  =             &= nbsp; 

P=   Think = green. Think before you print.

 <= /o:p>

 <= /o:p>

 

------=_NextPart_000_0027_01CFF299.003512B0-- From owner-chemistry@ccl.net Tue Oct 28 17:03:01 2014 From: "Igors Mihailovs igors.mihailovs0-x-gmail.com" To: CCL Subject: CCL: Problem with the convergence of Maximium and RMS displacement Message-Id: <-50652-141028170146-18993-RqaXVAH7qzpJaWbBFc/Wrg . server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=001a1141b5b025961e050681f430 Date: Tue, 28 Oct 2014 23:01:19 +0200 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0===gmail.com] --001a1141b5b025961e050681f430 Content-Type: text/plain; charset=UTF-8 Dear Radhika, As far as I know, increasing MaxCycles is usually not that thing one should begin with when dealing with convergence difficulties. What did I find helpful in such cases are * try initial guess from calculation with smaller basis set (use checkpoint file in that step, then Geom=Check Guess=TCheck in final optimization with the basis set desired); * try to plot the energy and maybe also the convergence criteria as a function of calculation step (simple line plot); if energy goes down smoothly and then begins to oscillate, You should probably try to perform new optimization starting from the last geometry before the calculation has gone fishing (with Geom=(Check, Step=N) Guess=TCheck); * or You can try Opt=CalcFC, as You will anyway need force constants for Your IR calculation (then You will be able to specify Freq=ReadFC); if that helps not, try Opt=CalcAll, but this is very heavy one; * of course, increasing MaxCycle also can help occasionally. With best regards, Igors Mihailovs, ISSP, University of Latvia 2014-10-28 9:40 GMT+02:00 Mariusz Radon mariusz.radon/agmail.com < owner-chemistry*_*ccl.net>: > > Sent to CCL by: Mariusz Radon [mariusz.radon_+_gmail.com] > On 10/28/2014 04:39 AM, Radhika Narayanan > radhika.narayanan.n|*|gmail.com wrote: > > Sent to CCL by: "Radhika Narayanan" [radhika.narayanan.n- -gmail.com] > > Dear all, > > > > I am dealing with the IR spectra of organometallic compounds.While doing > > the optimization using DFT functional, I encounter the following trouble: > > > > Maximum Force 0.000079 0.000450 YES > > RMS Force 0.000018 0.000300 YES > > Maximum Displacement 0.116059 0.001800 NO > > RMS Displacement 0.028645 0.001200 NO > > > > Error termination request processed by link 9999. > > > > However, optimization at HF level using the same basis set gave a > > converged geometry. > > > > Maximum Force 0.000004 0.000450 YES > > RMS Force 0.000001 0.000300 YES > > Maximum Displacement 0.001674 0.001800 YES > > RMS Displacement 0.000428 0.001200 YES > > > > What might be the reason for this error?Could anyone suggest a solution > > for this problem? > > > > Dear Radhika, > > Have you tried to increase the number of steps in geometry optimization > procedure? E.g., Opt(MaxCycles=300). > > Take care, > Mariusz> > > > > > -- > Dr Mariusz Radon, Ph.D. > Coordination Chemistry Group > Faculty of Chemistry > Jagiellonian University > ul. Ingardena 3, 30-060 Krakow, Poland > http://www2.chemia.uj.edu.pl/~mradon> > > --001a1141b5b025961e050681f430 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Radhika,

As far= as I know, increasing MaxCycles is usually not that thing one should begin= with when dealing with convergence difficulties. What did I find helpful i= n such cases are

* try initial guess from calculation with sm= aller basis set (use checkpoint file in that step, then Geom=3DCheck Guess= =3DTCheck in final optimization with the basis set desired);
* try= to plot the energy and maybe also the convergence criteria as a function o= f calculation step (simple line plot); if energy goes down smoothly and the= n begins to oscillate, You should probably try to perform new optimization = starting from the last geometry before the calculation has gone fishing (wi= th Geom=3D(Check, Step=3DN) Guess=3DTCheck);
* or You can try Opt= =3DCalcFC, as You will anyway need force constants for Your IR calculation = (then You will be able to specify Freq=3DReadFC); if that helps not, try Op= t=3DCalcAll, but this is very heavy one;
* of course, increasing M= axCycle also can help occasionally.

With best regards,
Igors Mihailovs,
ISSP, University of Latvia
=


2014-10-28 9:40 GMT+02:00 Mariusz Radon mari= usz.radon/agmail.com &l= t;owner-chemis= try*_*ccl.net>:

Sent to CCL by: Mariusz Radon [mariusz.radon_+_gmail.com]
On 10/28/2014 04:39 AM, Radhika Narayanan
radhika.narayanan.n|*|gmail.com wrote:
> Sent to CCL by: "Radhika=C2=A0 Narayanan" [radhika.narayanan= .n- -gmail.com]
> Dear all,
>
> I am dealing with the IR spectra of organometallic compounds.While doi= ng
> the optimization using DFT functional, I encounter the following troub= le:
>
>=C2=A0 Maximum Force=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.000079= =C2=A0 =C2=A0 =C2=A00.000450=C2=A0 =C2=A0 =C2=A0YES
>=C2=A0 RMS=C2=A0 =C2=A0 =C2=A0Force=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 0.000018=C2=A0 =C2=A0 =C2=A00.000300=C2=A0 =C2=A0 =C2=A0YES
>=C2=A0 Maximum Displacement=C2=A0 =C2=A0 =C2=A00.116059=C2=A0 =C2=A0 = =C2=A00.001800=C2=A0 =C2=A0 =C2=A0NO
>=C2=A0 RMS=C2=A0 =C2=A0 =C2=A0Displacement=C2=A0 =C2=A0 =C2=A00.028645= =C2=A0 =C2=A0 =C2=A00.001200=C2=A0 =C2=A0 =C2=A0NO
>
> Error termination request processed by link 9999.
>
> However, optimization at HF level using the same basis set gave a
> converged geometry.
>
>=C2=A0 Maximum Force=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.000004= =C2=A0 =C2=A0 =C2=A00.000450=C2=A0 =C2=A0 =C2=A0YES
>=C2=A0 RMS=C2=A0 =C2=A0 =C2=A0Force=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 0.000001=C2=A0 =C2=A0 =C2=A00.000300=C2=A0 =C2=A0 =C2=A0YES
>=C2=A0 Maximum Displacement=C2=A0 =C2=A0 =C2=A00.001674=C2=A0 =C2=A0 = =C2=A00.001800=C2=A0 =C2=A0 =C2=A0YES
>=C2=A0 RMS=C2=A0 =C2=A0 =C2=A0Displacement=C2=A0 =C2=A0 =C2=A00.000428= =C2=A0 =C2=A0 =C2=A00.001200=C2=A0 =C2=A0 =C2=A0YES
>
> What might be the reason for this error?Could anyone suggest a solutio= n
> for this problem?
>

Dear Radhika,

Have you tried to increase the number of steps in geometry optimization
procedure? E.g., Opt(MaxCycles=3D300).

Take care,
Mariusz>
>


--
Dr Mariusz Radon, Ph.D.
Coordination Chemistry Group
Faculty of Chemistry
Jagiellonian University
ul. Ingardena 3, 30-060 Krakow, Poland
http://w= ww2.chemia.uj.edu.pl/~mradon



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--001a1141b5b025961e050681f430-- From owner-chemistry@ccl.net Tue Oct 28 17:37:01 2014 From: "Violeta Isabel Perez Nueno pereznueno:-:harmonicpharma.com" To: CCL Subject: CCL: "Quantitative and Systems Pharmacology" at IWBBIO 2015, Granada, SPAIN Message-Id: <-50653-141028122645-14830-UREJTdP+emxyfK6IDhvQ+w[#]server.ccl.net> X-Original-From: "Violeta Isabel Perez Nueno" Date: Tue, 28 Oct 2014 12:26:43 -0400 Sent to CCL by: "Violeta Isabel Perez Nueno" [pereznueno : harmonicpharma.com] "Quantitative and Systems Pharmacology: Thinking in a wider "systems-level" context accelerates drug discovery and enlightens our understanding of drug action" at the 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2015), 15-17 April, 2015. Granada (SPAIN). http://iwbbio.ugr.es/ Quantitative and Systems Pharmacology (QSP) is an emerging discipline focused on identifying and validating drug targets, understanding existing therapeutics and discovering new ones. The goal of QSP is to understand, in a precise, predictive manner, how drugs modulate cellular networks in space and time and how they impact human pathophysiology. (QSP White Paper - October, 2011) Over the past three decades, the predominant paradigm in drug discovery was designing selective ligands for a specific target to avoid unwanted side effects. However, in the current post-genomic era, the aim is to design drugs that perturb biological networks rather than individual targets. The challenge is to be able to consider the complexity of physiological responses to treatments at very early stages of the drug development. In this way, current effort has been put into combining chemogenomics with network biology to implement new network-pharmacology approaches to drug discovery; i.e. polypharmacology approaches combined with systems biology information, which advance further in both improving efficacy and predicting unwanted off-target effects. Furthermore, the use of network biology to understand drug action outputs treasured information, i.e for pharmaceutical companies, such as alternative therapeutic indications for approved drugs, associations between proteins and drug side effects, drugdrug interactions, or pathways and gene associations which provide leads for new drug targets that may drive drug development. Following the line of QSP Workshops I and II (2008, 2010), the QSP White Paper (2011), or QSP Pittsburgh Workshop (2013), the goal of this symposium is to bring together interdisciplinary experts to help advance the understanding of how drugs act, with regard to their beneficial and toxic effects, by sharing new integrative, systems-based computational or experimental approaches/ tools / ideas which allow to increase the probability that the newly discovered drugs will prove therapeutically beneficial, together with a reduction in the risk of serious adverse events. A list of contributions with very high quality will be selected to be extended and submitted in different special issues (Biomedical Engineering Online (BMC), Current Bioinformatics, Genomics and Computational Biology, Current Topics in Medicinal Chemistry). More information can be found at: http://iwbbio.ugr.es/issues.php DEADLINE SUBMISSION OF PAPERS: November 30th, 2015 Submission must be done through the submission platform: https://easychair.org/conferences/? conf=iwbbio2015. There are two different categories for submissions: Full paper contributions (published under Lecture Notes in Bioinformatics (LNBI)) and Abstract contributions (published in the conference proceedings under both ISBN and ISSN references). More information can be found at: http://iwbbio.ugr.es/submissions.php IMPORTANT DATES: http://iwbbio.ugr.es/index.php You can learn more about IWBBIO by visiting the website http://iwbbio.ugr.es/index.php I am happy to answer any of your questions. Thank you. Best regards, Violeta Isabel Perez Nueno -- Violeta I. Perez-Nueno, Ph.D. Senior Scientist Harmonic Pharma 615 rue du Jardin Botanique 54600 Villers ls Nancy - France Cell +33(0) 638 878 547 ; Tel +33(0) 354 958 604 Fax +33(0) 383 275 652 pereznueno^harmonicpharma.com W:http://www.loria.fr/~pereznue/ www.harmonicpharma.com From owner-chemistry@ccl.net Tue Oct 28 18:12:01 2014 From: "James Robinson jameschums%%yahoo.com" To: CCL Subject: CCL: Problem with the convergence of Maximium and RMS displacement Message-Id: <-50654-141028175319-5885-qqGb/l9X8qiULCtcxl61fw||server.ccl.net> X-Original-From: "James Robinson" Date: Tue, 28 Oct 2014 17:53:18 -0400 Sent to CCL by: "James Robinson" [jameschums]|[yahoo.com] Dear Radhika If my terrible memory is still working, sometimes changing the step size using IOp(1/8=n) might help, I think the default is 30 (?) ..perhaps reduce this.. try this too.. http://www.ccl.net/chemistry/resources/messages/2002/07/09.006-dir/ Regards, James J J Robinson - personal email - opinions are personal only. From owner-chemistry@ccl.net Tue Oct 28 21:17:01 2014 From: "Brian Skinn bskinn,alum.mit.edu" To: CCL Subject: CCL:G: Problem with the convergence of Maximium and RMS displacement Message-Id: <-50655-141028211545-21414-62q+mcOdTVhGie3Iq3WBzg!=!server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=047d7b3a833c7b76bd050685808e Date: Tue, 28 Oct 2014 21:15:19 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [bskinn-*-alum.mit.edu] --047d7b3a833c7b76bd050685808e Content-Type: text/plain; charset=UTF-8 Radhika, I have had similar problems optimizing species with flat potential energy surfaces (e.g., nitromethane) with DFT in ORCA, where the forces are relatively small but the BFGS update algorithm executes disproportionately large steps. The approach I have used to address this is to tighten the quadrature grids (e.g., !GRID4 and !GRIDX9) and/or to constrain the trust region of the geometry optimization (e.g., %geom Trust -0.002 end). I unfortunately don't know the corresponding commands in Gaussian, though James's advice above sounds like it might pertain to the latter approach. I would guess the dramatic difference you are seeing in the behavior of HF vs DFT is due to the numerical quadrature required for DFT, which is absent in HF. Thus, tightening the quadrature grid might be the best place to start. Good luck, Brian On Tue, Oct 28, 2014 at 5:53 PM, James Robinson jameschums%%yahoo.com < owner-chemistry||ccl.net> wrote: > > Sent to CCL by: "James Robinson" [jameschums]|[yahoo.com] > Dear Radhika > > If my terrible memory is still working, sometimes changing the step size > using IOp(1/8=n) might help, I think the default is 30 (?) ..perhaps reduce > this.. try this too.. > > http://www.ccl.net/chemistry/resources/messages/2002/07/09.006-dir/ > > Regards, James > J J Robinson - personal email - opinions are personal only.> > > --047d7b3a833c7b76bd050685808e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Radhika,=C2=A0

I have had similar probl= ems optimizing species with flat potential energy surfaces (e.g., nitrometh= ane) with DFT in ORCA, where the forces are relatively small but the BFGS u= pdate algorithm executes disproportionately large steps.=C2=A0 The approach= I have used to address this is to tighten the quadrature grids (e.g., !GRI= D4 and !GRIDX9) and/or to constrain the trust region of the geometry optimi= zation (e.g., %geom Trust -0.002 end).=C2=A0 I unfortunately don't know= the corresponding commands in Gaussian, though James's advice above so= unds like it might pertain to the latter approach.

I wou= ld guess the dramatic difference you are seeing in the behavior of HF vs DF= T is due to the numerical quadrature required for DFT, which is absent in H= F.=C2=A0 Thus, tightening the quadrature grid might be the best place to st= art.


Good luck,
Brian

On = Tue, Oct 28, 2014 at 5:53 PM, James Robinson jameschums%%yahoo.com <owner-chemistry||ccl.net> wro= te:

Sent to CCL by: "James=C2=A0 Robinson" [jameschums]|[yahoo.com]
Dear Radhika

If my terrible memory is still working, sometimes changing the step size us= ing IOp(1/8=3Dn) might help, I think the default is 30 (?) ..perhaps reduce= this.. try this too..

http://www.ccl.net/chemistry/resources/messages/2002= /07/09.006-dir/

Regards, James
J J Robinson - personal email - opinions are personal only.



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