From owner-chemistry@ccl.net Wed Jul 15 07:14:01 2015 From: "Jan H Jensen jhjensen[]chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlights: June issue Message-Id: <-51536-150715033044-25826-9T0nL3cROnL39mbFVvkYug^server.ccl.net> X-Original-From: "Jan H Jensen" Date: Wed, 15 Jul 2015 03:30:43 -0400 Sent to CCL by: "Jan H Jensen" [jhjensen+/-chem.ku.dk] The June issue of Computational Chemistry Highlights is out. http://www.compchemhighlights.org/2015_06_01_archive.html CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here. Table of content for this issue features contributions from CCH editors Steven Bachrach, Tobias Schwabe and Jan Jensen: Accurately Modeling Nanosecond Protein Dynamics Requires at least Microseconds of Simulation http://www.compchemhighlights.org/2015/06/accurately-modeling-nanosecond-protein.html A Practicable Real-Space Measure and Visualization of Static Electron-Correlation Effects http://www.compchemhighlights.org/2015/06/a-practicable-real-space-measure-and.html Ring Planarity Problem of 2-Oxazoline Revisited Using Microwave Spectroscopy and Quantum Chemical Calculations http://www.compchemhighlights.org/2015/06/ring-planarity-problem-of-2-oxazoline.html Charge-Enhanced Acidity and Catalyst Activation http://www.compchemhighlights.org/2015/06/charge-enhanced-acidity-and-catalyst.html Interested in more? There are many ways to subscribe to CCH updates. http://www.compchemhighlights.org/p/get-cch-updates.html Also, for your daily computational chemistry fix subscribe to Computational Chemistry Daily https://paper.li/janhjensen/1416314690 From owner-chemistry@ccl.net Wed Jul 15 15:34:00 2015 From: "Joy Ku joyku!^!stanford.edu" To: CCL Subject: CCL: Macromolecular Simulation Software Workshop featuring OpenMM Message-Id: <-51537-150715152037-19897-d/3SCY4FZw7ewJJJDPi/3A_._server.ccl.net> X-Original-From: "Joy Ku" Date: Wed, 15 Jul 2015 15:20:36 -0400 Sent to CCL by: "Joy Ku" [joyku++stanford.edu] Macromolecular Simulation Software Workshop Dates: October 12, 2015 to October 25, 2015 Location: CECAM-DE-JUELICH, Juelich, Germany Application deadline: July 27, 2015. Each sub-workshop is limited to 30 participants Registration and more information: http://www.cecam.org/workshop-1214.html Description Biomolecular simulation continues to grow in popularity and scope of application. It is no longer the preserve of a few specialist groups but is widespread - part of the toolkit used by researchers in a wide variety of fields, often closely integrated with other experimental research techniques. As the use of biomolecular simulation grows, a corresponding boom in (decentralised) software development is taking place. This workshop is formatted as six sequential workshops, each 2 days long, that enable participants to learn about many different aspects of biomolecular simulation software: * Software development and engineering * Simulation data analysis * Setting up simulations * Development of software libraries * High-performance distributed computing tools * Advanced sampling and long timescale molecular dynamics. Participants will be able to attend all sub-workshops or just a subset of them. In the process, they will learn about many biomolecular simulation software that are available, including: * OpenMM (https://simtk.org/home/openmm), * MMTK (http://dirac.cnrs-orleans.fr/MMTK/), * MDAnalysis (https://code.google.com/p/mdanalysis/) , * MDTraj (http://mdtraj.org/latest/), * SIRE (http://siremol.org/Sire/Home.html), * Bookshelf (http://sbcb.bioch.ox.ac.uk/bookshelf/) as well as more general-purpose Python-based tools that have clear applicability to biosimulation e.g. RADICAL-Cybertools (http://radical-cybertools.github.com). To register or learn more about the workshop, visit http://www.cecam.org/workshop-1214.html. Costs There is no registration fee for the workshop, but accommodation, meals and all other travel costs must be covered by participants. Some funding may be provided by NSF to enable US early career researchers to attend the workshop. From owner-chemistry@ccl.net Wed Jul 15 16:11:00 2015 From: "Igors Mihailovs igors.mihailovs0[]gmail.com" To: CCL Subject: CCL:G: M06L with D3 correction Message-Id: <-51538-150715160858-481-WeKqKlUJS7nlRWV2KivmJQ__server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=001a113aa82604cee3051aef866e Date: Wed, 15 Jul 2015 23:08:32 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0===gmail.com] --001a113aa82604cee3051aef866e Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear All, Thank You for Your advices, they have indeed aided me in my research, and I wish the same for Mr. Gupta :) Considering my reply, it was based on the year 2014 review by Peverati and Truhlar that states, among all, that: "[..] in the parametrization of the TS-vdW model, where the =E2=80=98disper= sion=E2=80=99 terms were damped at a larger distance for M06 and M06-L than for six other studied functionals [85] because the Minnesota functionals already included more attractive non-covalent interactions at van der Waals distances." which I managed to misunderstand (thinking that six other functionals come > from the review, not the reference 85). However, this review also states that: "two local functionals developed in Minnesota (M11-L and MN12-L) are more accurate than M06-L for non-covalent complexation energies, and five non-local functionals developed in Minnesota (M06-2X, M08-HX, M08-SO, M11 and MN12-SX) are more accurate than M06 for non-covalent complexation energies" So, why shouldn't Mr. Gupta consider these newer functionals? I know firmly that, for example, M11-L, MN12-L and M06-2X are available in Gaussian 09, rev. D.01. Hope there was something useful, Igors Mihailovs (engineer) Institute of Solid State Physics University of Latvia 2015-07-15 2:10 GMT+03:00 Lars Goerigk lars.goerigk _ unimelb.edu.au < owner-chemistry(_)ccl.net>: > Dear Mr Gupta, > > M06-L does not describe the asymptotic behaviour of the London dispersion > energy correctly and the consequences of this have been shown here: > > Chem. Phys. Chem. 2011, 12, 3421. > > Therefore, it can benefit from being combined with a dispersion > correction. However, due to the fact that it contains many parameters > fitted to noncovalent interaction energies, double-counting effects have > been observed in the medium-range regime > when it is combined with the Becke-Johnson damping function for DFT-D3. > Therefore, it was only compatible with the zero-damping version, as > described in: > > PCCP 2011, 13, 6670. > > > I hope this helped. > > Regards, > Lars > --- > Dr. Lars Goerigk > ARC DECRA Fellow > School of Chemistry > The University of Melbourne > VIC 3010 > Australia > > Research profile: > http://www.chemistry.unimelb.edu.au/dr-lars-goerigk > List of my publications: > http://www.researcherid.com/rid/D-3717-2009 > Follow me on Twitter: https://twitter.com/lgoer_compchem > > On 15 Jul 2015, at 12:51 am, Puneet Gupta puneetg.iitk/./gmail.com< > http://gmail.com> ccl.net>> wrote: > > > Sent to CCL by: "Puneet Gupta" [puneetg.iitk : gmail.com >] > Dear All, > > Is it important to add D3 correction in M06L functional? Please guide me > with your suggestion. The system I am working on contains hydrogen bondin= g > interactions. > > Thanks! > > Kind regards, > Puneet > > > > -=3D This is automatically added to each message by the mailing script > =3D-E-mail to subscribers: CHEMISTRY!^!ccl.net > or use:E-mail to administrators: CHEMISTRY-REQUEST!^!ccl.net CHEMISTRY-REQUEST!^!ccl.net> or usehttp:// > www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_00= 0_E981B13824164CE0A6BBBAD6599FCE3Bunimelbeduau_ > Content-Type: text/html; charset"us-ascii" > Content-ID: > Content-Transfer-Encoding: quoted-printable > > > > > > -webkit-line-break: after-white-space;"> > Dear Mr Gupta, >

>
>
M06-L does not describe the asymptotic behaviour of the London > dispersion energy correctly and the consequences of this have been shown > here:
>

>
>
Chem. Phys. Chem.  2011, 12, 3421.
>

>
>
Therefore, it can benefit from being combined with a dispersion > correction. However, due to the fact that it contains many parameters > fitted to noncovalent interaction energies, double-counting effects have > been observed in the medium-range regime
>
when it is combined with the Becke-Johnson damping function for > DFT-D3. Therefore, it was only compatible with the zero-damping version, = as > described in:
>

>
>
PCCP 2011, 13, 6670.
>

>
>

>
>
I hope this helped.
>

>
>
Regards,
>
Lars
>
>
text-align: start; text-indent: 0px; text-transform: none; white-space: > normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; > word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: > after-white-space;"> >
text-align: start; text-indent: 0px; text-transform: none; white-space: > normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; > word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: > after-white-space;"> >
-webkit-line-break: after-white-space;"> >
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > ---
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > Dr. Lars Goerigk
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > ARC DECRA Fellow
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > School of Chemistry
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > The University of Melbourne
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > VIC 3010
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > Australia
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >
>
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > Research profile: 
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > > http://www.chemistry.unimelb.edu.au/dr-lars-goerigk
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > List of my publications:
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > > http://www.researcherid.com/rid/D-3717-2009
>
font-style: normal; font-variant: normal; font-weight: normal; > letter-spacing: normal; line-height: normal; orphans: auto; text-align: > start; text-indent: 0px; text-transform: none; white-space: normal; widow= s: > auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> > Follow me on Twitter: > https://twitter.com/lgoer_compchem
>
>
>
>
>
>
>
On 15 Jul 2015, at 12:51 am, Puneet Gupta puneetg.iitk/./ http://gmail.com">gmail.com < ccl.net">owner-chemistry!^!ccl.net> wrote:
>
>

> Sent to CCL by: "Puneet  Gupta" [puneetg.iitk : http://gmail.com">gmail.com]
> Dear All,
>
> Is it important to add D3 correction in M06L functional? Please guide me > with your suggestion. The system I am working on contains hydrogen bondin= g > interactions. >
>
> Thanks!
>
> Kind regards,
> Puneet
>
>
>
> -=3D This is automatically added to each message by the mailing script > =3D- >
> E-mail to subscribers: CHEMISTRY!^= ! > ccl.net or use:
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> > > --001a113aa82604cee3051aef866e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear All,

Thank You for Your advices, t= hey have indeed aided me in my research, and I wish the same for Mr. Gupta = :)
Considering my reply, it was based on the year 2014 review by = Peverati and Truhlar that states, among all, that:

"[..] in the parametrization of the TS-vdW model, where the =E2=80=98= dispersion=E2=80=99 terms were damped at a larger distance for M06 and M06-= L than for six other studied functionals [85] because the Minnesota functio= nals already included more attractive non-covalent interactions at van der = Waals distances."

which I managed to misunder= stand (thinking that six other functionals come from the review, not the re= ference 85). However, this review also states that:

"two local functionals developed in Minnesota (M11-L and MN12-L) are= more accurate than M06-L for non-covalent complexation energies, and five = non-local functionals developed in Minnesota (M06-2X, M08-HX, M08-SO, M11 a= nd MN12-SX) are more accurate than M06 for non-covalent complexation energi= es"

So, why shouldn't Mr. Gupta consider = these newer functionals? I know firmly that, for example, M11-L, MN12-L and= M06-2X are available in Gaussian 09, rev. D.01.


=
Hope there was something useful= ,
Igors Mihailovs (engineer)
Institute of Solid= State Physics
University of Latvia

<= /div>

2015-07-15 2:10 GMT+03:00 Lars Goerigk lars.= goerigk _ unimelb.edu.au <owne= r-chemistry(_)ccl.net>:
Dear = Mr Gupta,

M06-L does not describe the asymptotic behaviour of the London dispersion e= nergy correctly and the consequences of this have been shown here:

Chem. Phys. Chem.=C2=A0 2011, 12, 3421.

Therefore, it can benefit from being combined with a dispersion correction.= However, due to the fact that it contains many parameters fitted to noncov= alent interaction energies, double-counting effects have been observed in t= he medium-range regime
when it is combined with the Becke-Johnson damping function for DFT-D3. The= refore, it was only compatible with the zero-damping version, as described = in:

PCCP 2011, 13, 6670.


I hope this helped.

Regards,
Lars
---
Dr. Lars Goerigk
ARC DECRA Fellow
School of Chemistry
The University of Melbourne
VIC 3010
Australia

Research profile:
http://www.chemistry.unimelb.edu.au/dr-lars-goeri= gk
List of my publications:
http://www.researcherid.com/rid/D-3717-2009
Follow me on Twitter: https://twitter.com/lgoer_compchem

On 15 Jul 2015, at 12:51 am, Puneet Gupta puneetg.iitk/./gmail.com<http://gmail.com> <owner-chemistry!^!ccl.net<mailto:o= wner-chemistry!^!ccl.net>> wrote:


Sent to CCL by: "Puneet=C2=A0 Gupta" [puneetg.iitk : gmail.com<http://gmail.= com>]
Dear All,

Is it important to add D3 correction in M06L functional? Please guide me wi= th your suggestion. The system I am working on contains hydrogen bonding in= teractions.

Thanks!

Kind regards,
Puneet



-=3D This is automatically added to each message by the mailing scri= pt =3D-E-mail to subscribers: CHEMISTRY!^!ccl.net<mailto:CHEMISTRY!^!ccl.net> or use:E-mail to administrators: CHEMISTRY-REQU= EST!^!ccl.n= et<mailto:CHEMISTRY-REQUEST= !^!ccl.net<= /a>> or usehttp://www.ccl.net/chemistry/su= b_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_E981B13824164CE0A6BBBAD6= 599FCE3Bunimelbeduau_
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</head>
<body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; -we= bkit-line-break: after-white-space;">
Dear Mr Gupta,
<div><br>
</div>
<div>M06-L does not describe the asymptotic behaviour of the London d= ispersion energy correctly and the consequences of this have been shown her= e:</div>
<div><br>
</div>
<div>Chem. Phys. Chem. &nbsp;2011, 12, 3421.</div>
<div><br>
</div>
<div>Therefore, it can benefit from being combined with a dispersion = correction. However, due to the fact that it contains many parameters fitte= d to noncovalent interaction energies, double-counting effects have been ob= served in the medium-range regime</div>
<div>when it is combined with the Becke-Johnson damping function for = DFT-D3. Therefore, it was only compatible with the zero-damping version, as= described in:</div>
<div><br>
</div>
<div>PCCP 2011, 13, 6670.</div>
<div><br>
</div>
<div><br>
</div>
<div>I hope this helped.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Lars</div>
<div apple-content-edited=3D"true">
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans:= auto; text-align: start; text-indent: 0px; text-transform: none; white-spa= ce: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px= ; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: afte= r-white-space;">
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans:= auto; text-align: start; text-indent: 0px; text-transform: none; white-spa= ce: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px= ; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: afte= r-white-space;">
<div style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; -web= kit-line-break: after-white-space;">
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
---</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
Dr. Lars Goerigk</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
ARC DECRA Fellow</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
School of Chemistry</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
The University of Melbourne</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
VIC 3010</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
Australia</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<br>
</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
Research profile:&nbsp;</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<a href=3D"http://www.chemistry.unimelb.e= du.au/dr-lars-goerigk">http://www.che= mistry.unimelb.edu.au/dr-lars-goerigk</a></div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
List of my publications:</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<a href=3D"http://www.researcherid.com/rid/D-3717= -2009">http://www.researcherid.com/rid/D-3717= -2009</a></div>
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Follow me on Twitter: <a href=3D"https://twitter.com/lgoer= _compchem">https://twitter.com/lgoer_compchem<= ;/a></div>
</div>
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<div>On 15 Jul 2015, at 12:51 am, Puneet Gupta puneetg.iitk/./<a h= ref=3D"http://gmail.com">gmail.com</a> &lt;<a href=3D"= mailto:owner-chemistry!^!ccl.net">o= wner-chemistry!^!ccl.net</a>&gt; wrote:</div>
<br class=3D"Apple-interchange-newline">
<blockquote type=3D"cite"><br>
Sent to CCL by: &quot;Puneet &nbsp;Gupta&quot; [puneetg.iitk : = <a href=3D"http://gmail.com">gmail.com</a>]<br>
Dear All,<br>
<br>
Is it important to add D3 correction in M06L functional? P= lease guide me with your suggestion. The system I am working on contains hy= drogen bonding interactions.
<br>
<br>
Thanks!<br>
<br>
Kind regards,<br>
Puneet<br>
<br>
<br>
<br>
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--001a113aa82604cee3051aef866e-- From owner-chemistry@ccl.net Wed Jul 15 17:57:00 2015 From: "Puneet Gupta puneetg.iitk++gmail.com" To: CCL Subject: CCL:G: M06L with D3 correction Message-Id: <-51539-150715175635-21185-TEM+QCqOohK9HgpMIymT9Q::server.ccl.net> X-Original-From: Puneet Gupta Content-Type: multipart/alternative; boundary=047d7bfcf01ed8ae8a051af1067b Date: Wed, 15 Jul 2015 23:56:27 +0200 MIME-Version: 1.0 Sent to CCL by: Puneet Gupta [puneetg.iitk[-]gmail.com] --047d7bfcf01ed8ae8a051af1067b Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear All, Thank you very much for your suggestions! The advices are indeed helpful for my understanding. Thanks Mr. Mihailovs for drawing my attention to the newer Minnesota DFT functionals. Kind regards, Puneet Gupta On Wed, Jul 15, 2015 at 10:08 PM, Igors Mihailovs igors.mihailovs0[] gmail.com wrote: > Dear All, > > Thank You for Your advices, they have indeed aided me in my research, and > I wish the same for Mr. Gupta :) > Considering my reply, it was based on the year 2014 review by Peverati an= d > Truhlar that states, among all, that: > > "[..] in the parametrization of the TS-vdW model, where the =E2=80=98disp= ersion=E2=80=99 > terms were damped at a larger distance for M06 and M06-L than for six oth= er > studied functionals [85] because the Minnesota functionals already includ= ed > more attractive non-covalent interactions at van der Waals distances." > > which I managed to misunderstand (thinking that six other functionals com= e > from the review, not the reference 85). However, this review also states > that: > > "two local functionals developed in Minnesota (M11-L and MN12-L) are more > accurate than M06-L for non-covalent complexation energies, and five > non-local functionals developed in Minnesota (M06-2X, M08-HX, M08-SO, M11 > and MN12-SX) are more accurate than M06 for non-covalent complexation > energies" > > So, why shouldn't Mr. Gupta consider these newer functionals? I know > firmly that, for example, M11-L, MN12-L and M06-2X are available in > Gaussian 09, rev. D.01. > > > Hope there was something useful, > Igors Mihailovs (engineer) > Institute of Solid State Physics > University of Latvia > > > 2015-07-15 2:10 GMT+03:00 Lars Goerigk lars.goerigk _ unimelb.edu.au < > owner-chemistry##ccl.net>: > >> Dear Mr Gupta, >> >> M06-L does not describe the asymptotic behaviour of the London dispersio= n >> energy correctly and the consequences of this have been shown here: >> >> Chem. Phys. Chem. 2011, 12, 3421. >> >> Therefore, it can benefit from being combined with a dispersion >> correction. However, due to the fact that it contains many parameters >> fitted to noncovalent interaction energies, double-counting effects have >> been observed in the medium-range regime >> when it is combined with the Becke-Johnson damping function for DFT-D3. >> Therefore, it was only compatible with the zero-damping version, as >> described in: >> >> PCCP 2011, 13, 6670. >> >> >> I hope this helped. >> >> Regards, >> Lars >> --- >> Dr. Lars Goerigk >> ARC DECRA Fellow >> School of Chemistry >> The University of Melbourne >> VIC 3010 >> Australia >> >> Research profile: >> http://www.chemistry.unimelb.edu.au/dr-lars-goerigk >> List of my publications: >> http://www.researcherid.com/rid/D-3717-2009 >> Follow me on Twitter: https://twitter.com/lgoer_compchem >> >> On 15 Jul 2015, at 12:51 am, Puneet Gupta puneetg.iitk/./gmail.com< >> http://gmail.com> > ccl.net>> wrote: >> >> >> Sent to CCL by: "Puneet Gupta" [puneetg.iitk : gmail.com< >> http://gmail.com>] >> Dear All, >> >> Is it important to add D3 correction in M06L functional? Please guide me >> with your suggestion. The system I am working on contains hydrogen bondi= ng >> interactions. >> >> Thanks! >> >> Kind regards, >> Puneet >> >> >> >> -=3D This is automatically added to each message by the mailing script >> =3D-E-mail to subscribers: CHEMISTRY!^!ccl.net >> or use:E-mail to administrators: CHEMISTRY-REQUEST!^!ccl.net> CHEMISTRY-REQUEST!^!ccl.net> or usehttp:// >> www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_0= 00_E981B13824164CE0A6BBBAD6599FCE3Bunimelbeduau_ >> Content-Type >> : >> text/html; charset"us-ascii" >> Content-ID: >> Content-Transfer-Encoding: quoted-printable >> >> >> >> >> >> > -webkit-line-break: after-white-space;"> >> Dear Mr Gupta, >>

>>
>>
M06-L does not describe the asymptotic behaviour of the London >> dispersion energy correctly and the consequences of this have been shown >> here:
>>

>>
>>
Chem. Phys. Chem.  2011, 12, 3421.
>>

>>
>>
Therefore, it can benefit from being combined with a dispersion >> correction. However, due to the fact that it contains many parameters >> fitted to noncovalent interaction energies, double-counting effects have >> been observed in the medium-range regime
>>
when it is combined with the Becke-Johnson damping function for >> DFT-D3. Therefore, it was only compatible with the zero-damping version,= as >> described in:
>>

>>
>>
PCCP 2011, 13, 6670.
>>

>>
>>

>>
>>
I hope this helped.
>>

>>
>>
Regards,
>>
Lars
>>
>>
> text-align: start; text-indent: 0px; text-transform: none; white-space: >> normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; >> word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: >> after-white-space;"> >>
> text-align: start; text-indent: 0px; text-transform: none; white-space: >> normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; >> word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: >> after-white-space;"> >>
> -webkit-line-break: after-white-space;"> >>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> ---
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> Dr. Lars Goerigk
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> ARC DECRA Fellow
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> School of Chemistry
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> The University of Melbourne
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> VIC 3010
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> Australia
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >>
>>
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> Research profile: 
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> >> http://www.chemistry.unimelb.edu.au/dr-lars-goerigk
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> List of my publications:
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> >> http://www.researcherid.com/rid/D-3717-2009
>>
> font-style: normal; font-variant: normal; font-weight: normal; >> letter-spacing: normal; line-height: normal; orphans: auto; text-align: >> start; text-indent: 0px; text-transform: none; white-space: normal; wido= ws: >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> >> Follow me on Twitter: >> https://twitter.com/lgoer_compchem
>>
>>
>>
>>
>>
>>
>>
On 15 Jul 2015, at 12:51 am, Puneet Gupta puneetg.iitk/./> http://gmail.com">gmail.com <> ccl.net">owner-chemistry!^!ccl.net> wrote:
>>
>>

>> Sent to CCL by: "Puneet  Gupta" [puneetg.iitk : > http://gmail.com">gmail.com]
>> Dear All,
>>
>> Is it important to add D3 correction in M06L functional? Please guide me >> with your suggestion. The system I am working on contains hydrogen bondi= ng >> interactions. >>
>>
>> Thanks!
>>
>> Kind regards,
>> Puneet
>>
>>
>>
>> -=3D This is automatically added to each message by the mailing script >> =3D- >>
>> E-mail to subscribers: CHEMISTRY!= ^! >> ccl.net or use:
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>>      
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>> >> >> > > --047d7bfcf01ed8ae8a051af1067b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear All,

Thank you very much = for your suggestions! The advices are indeed helpful for my understanding. =

Thanks Mr. Mihailovs for drawing my attention to the newer Minnesot= a DFT functionals.

Kind regards,
Puneet Gupta

On Wed, Jul 15= , 2015 at 10:08 PM, Igors Mihailovs igors.mihailovs0[]gmail.com <owner-chemistry#,#ccl.net> wrote:=
Dear All,

Thank You for Your advices, they have indeed aided me in my research,= and I wish the same for Mr. Gupta :)
Considering my reply, it wa= s based on the year 2014 review by Peverati and Truhlar that states, among = all, that:

"[..] in the parametrization of th= e TS-vdW model, where the =E2=80=98dispersion=E2=80=99 terms were damped at= a larger distance for M06 and M06-L than for six other studied functionals= [85] because the Minnesota functionals already included more attractive no= n-covalent interactions at van der Waals distances."

which I managed to misunderstand (thinking that six other functiona= ls come from the review, not the reference 85). However, this review also s= tates that:

"two local functionals developed = in Minnesota (M11-L and MN12-L) are more accurate than M06-L for non-covale= nt complexation energies, and five non-local functionals developed in Minne= sota (M06-2X, M08-HX, M08-SO, M11 and MN12-SX) are more accurate than M06 f= or non-covalent complexation energies"

So, wh= y shouldn't Mr. Gupta consider these newer functionals? I know firmly t= hat, for example, M11-L, MN12-L and M06-2X are available in Gaussian 09, re= v. D.01.


<= div>
Hope there was somethi= ng useful,
Igors Mihailovs (engineer)
Institute= of Solid State Physics
University of Latvia

2015-07-15 2:10 GMT+03:00 Lars Goerigk lars.= goerigk _ unimelb.edu.a= u <owner-chemistry##ccl.net>:
Dear Mr Gupta,

M06-L does not describe the asymptotic behaviour of the London dispersion e= nergy correctly and the consequences of this have been shown here:

Chem. Phys. Chem.=C2=A0 2011, 12, 3421.

Therefore, it can benefit from being combined with a dispersion correction.= However, due to the fact that it contains many parameters fitted to noncov= alent interaction energies, double-counting effects have been observed in t= he medium-range regime
when it is combined with the Becke-Johnson damping function for DFT-D3. The= refore, it was only compatible with the zero-damping version, as described = in:

PCCP 2011, 13, 6670.


I hope this helped.

Regards,
Lars
---
Dr. Lars Goerigk
ARC DECRA Fellow
School of Chemistry
The University of Melbourne
VIC 3010
Australia

Research profile:
http://www.chemistry.unimelb.edu.au/dr-lars-goeri= gk
List of my publications:
http://www.researcherid.com/rid/D-3717-2009
Follow me on Twitter: https://twitter.com/lgoer_compchem

On 15 Jul 2015, at 12:51 am, Puneet Gupta puneetg.iitk/./gmail.com<http://gmail.com> <owner-chemistry!^!ccl.net<mailto:owner-chemistry!^!ccl.net>> wrote:


Sent to CCL by: "Puneet=C2=A0 Gupta" [puneetg.iitk : gmail.com<http://gmail.= com>]
Dear All,

Is it important to add D3 correction in M06L functional? Please guide me wi= th your suggestion. The system I am working on contains hydrogen bonding in= teractions.

Thanks!

Kind regards,
Puneet



-=3D This is automatically added to each message by the mailing scri= pt =3D-E-mail to subscribers: CHEMISTRY!^!ccl.net<mailto:CHEMISTRY!^!ccl.net> or use:E-mail to administrato= rs: CHEMISTRY-REQUEST!^!ccl.net<mailto:CHEMISTRY-REQUEST!^!ccl.net> or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.ne= t/spammers.txt--_000_E981B13824164CE0A6BBBAD6599FCE3Bunimelbeduau_
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Dear Mr Gupta,
<div><br>
</div>
<div>M06-L does not describe the asymptotic behaviour of the London d= ispersion energy correctly and the consequences of this have been shown her= e:</div>
<div><br>
</div>
<div>Chem. Phys. Chem. &nbsp;2011, 12, 3421.</div>
<div><br>
</div>
<div>Therefore, it can benefit from being combined with a dispersion = correction. However, due to the fact that it contains many parameters fitte= d to noncovalent interaction energies, double-counting effects have been ob= served in the medium-range regime</div>
<div>when it is combined with the Becke-Johnson damping function for = DFT-D3. Therefore, it was only compatible with the zero-damping version, as= described in:</div>
<div><br>
</div>
<div>PCCP 2011, 13, 6670.</div>
<div><br>
</div>
<div><br>
</div>
<div>I hope this helped.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Lars</div>
<div apple-content-edited=3D"true">
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans:= auto; text-align: start; text-indent: 0px; text-transform: none; white-spa= ce: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px= ; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: afte= r-white-space;">
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans:= auto; text-align: start; text-indent: 0px; text-transform: none; white-spa= ce: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px= ; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: afte= r-white-space;">
<div style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; -web= kit-line-break: after-white-space;">
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
---</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
Dr. Lars Goerigk</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
ARC DECRA Fellow</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
School of Chemistry</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
The University of Melbourne</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
VIC 3010</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
Australia</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-siz= e: 12px; font-style: normal; font-variant: normal; font-weight: normal; let= ter-spacing: normal; line-height: normal; orphans: auto; text-align: start;= text-indent: 0px; text-transform: none; white-space: normal; widows: auto;= word-spacing: 0px; -webkit-text-stroke-width: 0px;">
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Research profile:&nbsp;</div>
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<a href=3D"http://www.chemistry.unimelb.e= du.au/dr-lars-goerigk">http://www.che= mistry.unimelb.edu.au/dr-lars-goerigk</a></div>
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List of my publications:</div>
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<a href=3D"http://www.researcherid.com/rid/D-3717= -2009">http://www.researcherid.com/rid/D-3717= -2009</a></div>
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Follow me on Twitter: <a href=3D"https://twitter.com/lgoer= _compchem">https://twitter.com/lgoer_compchem<= ;/a></div>
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<div>On 15 Jul 2015, at 12:51 am, Puneet Gupta puneetg.iitk/./<a h= ref=3D"http://gmail.com">gmail.com</a> &lt;<a href=3D"= mailto:owner-chemistry= !^!ccl.= net">owner-chemistry!^!ccl.net</a>&gt; wrote:</div> <br class=3D"Apple-interchange-newline">
<blockquote type=3D"cite"><br>
Sent to CCL by: &quot;Puneet &nbsp;Gupta&quot; [puneetg.iitk : = <a href=3D"http://gmail.com">gmail.com</a>]<br>
Dear All,<br>
<br>
Is it important to add D3 correction in M06L functional? Please guide= me with your suggestion. The system I am working on contains hydrogen bond= ing interactions.
<br>
<br>
Thanks!<br>
<br>
Kind regards,<br>
Puneet<br>
<br>
<br>
<br>
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