From owner-chemistry@ccl.net Fri Sep 28 07:21:00 2012 From: "Mariusz Radon mariusz.radon]^[gmail.com" To: CCL Subject: CCL: interaction energy Message-Id: <-47686-120928065554-23996-ukTunfjnm+qrDsvLwUZNXA%x%server.ccl.net> X-Original-From: Mariusz Radon Content-Type: text/plain; charset=UTF-8 Date: Fri, 28 Sep 2012 12:55:47 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon^_^gmail.com] Dear CCLers, let me join this thread and ask a question, addressed mostly to Bradley: On Wed, Sep 26, 2012 at 8:29 PM, Bradley Welch bwelch5(!)slu.edu wrote: > Before anything else I would highly consider doing a BSSE computation. The > pople basis sets are prone to significant BSSE. > (...) > Then apply the zero point correction (calculated with BSSE!). Of course, I fully agree that BSSE is crucial, especially in ab initio calculation with small basis set, like MP2/6-31G here. (By the way, this basis is clearly too small for MP2!) But I have never calculated zero-point correction with BSSE included: i.e., frequency calculations for A with dummy atoms on B instead of "normal" frequency calculations for A. Do you have any experience and comparison, suggesting that not including dummy atoms in frequency calculations is really important (i.e., producing an energy difference larger than ~0.1 kcal/mol)? Kind regards, Mariusz Radon On Wed, Sep 26, 2012 at 8:29 PM, Bradley Welch bwelch5(!)slu.edu wrote: > Before anything else I would highly consider doing a BSSE computation. The > pople basis sets are prone to significant BSSE. > > So what I would do if I had the resources is redo your calculation with the > BSSE correction. To get the A-B interaction you would do the following > > > AB= (AB+zp) - ((A+zp) +(B+zp)) > > On Tue, Sep 25, 2012 at 11:17 PM, shekhar mittal sumitmittal49 a gmail.com > wrote: >> >> >> Sent to CCL by: "shekhar mittal" [sumitmittal49(_)gmail.com] >> Hi, >> It is a bit trivial problem but I am quite stuck with it. I have performed >> ab initio calculations for a complex (A-B) and its components (A and B) at >> the MP2/6-31G level of theory. In the output file, I get energy for each >> molecule listed as E(MP2). From frequency calculations, I got zero-point >> corrections. >> So my question is that while calculating interaction (or stabilization) >> energy, we use De (i.e. E(MP2)) or Do( E(MP2)-zero point energy correction)?>> E-mail to subscribers: CHEMISTRY]![ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST]![ccl.net or use>> >> > > > > -- > Bradley Welch > Saint Louis University > Monsanto Hall Room 218 > From owner-chemistry@ccl.net Fri Sep 28 10:13:00 2012 From: "Sergio Antonio Rodriguez drsergiorod/a\gmail.com" To: CCL Subject: CCL: help with a calculation Message-Id: <-47687-120928094437-8489-zxPkld6sLH5WPTvgKCowpA-#-server.ccl.net> X-Original-From: "Sergio Antonio Rodriguez" Date: Fri, 28 Sep 2012 09:44:35 -0400 Sent to CCL by: "Sergio Antonio Rodriguez" [drsergiorod[*]gmail.com] Hello! I need obtain the spin density values, for example in the HOMO, How I must do to obtain them? I know locate the mulliken coeficients of each atom and orbital. must I apply an equation? Thanks a lot. From owner-chemistry@ccl.net Fri Sep 28 12:04:01 2012 From: "Bradley Welch bwelch5 .. slu.edu" To: CCL Subject: CCL: interaction energy Message-Id: <-47688-120928120309-9665-QAooQ84a8tchHjkmE0PvWw],[server.ccl.net> X-Original-From: Bradley Welch Content-Type: multipart/alternative; boundary=20cf307ca386adec3e04cac53046 Date: Fri, 28 Sep 2012 11:03:00 -0500 MIME-Version: 1.0 Sent to CCL by: Bradley Welch [bwelch5:_:slu.edu] --20cf307ca386adec3e04cac53046 Content-Type: text/plain; charset=ISO-8859-1 Mariusz, I think you're right actually. Thermodynamics probably would not be that sensitive to a slight change in total energy due to the bsse calculation. My first thought when I saw his question was treat everything the same. If you do a bsse for one part you do a bsse for the entire set of calculations, including your frequency calculations. That though process itself is probably a beginners mistake. On Fri, Sep 28, 2012 at 5:55 AM, Mariusz Radon mariusz.radon]^[gmail.com < owner-chemistry{:}ccl.net> wrote: > > Sent to CCL by: Mariusz Radon [mariusz.radon^_^gmail.com] > Dear CCLers, > let me join this thread and ask a question, addressed mostly to Bradley: > > On Wed, Sep 26, 2012 at 8:29 PM, Bradley Welch bwelch5(!)slu.edu > wrote: > > Before anything else I would highly consider doing a BSSE computation. > The > > pople basis sets are prone to significant BSSE. > > (...) > > Then apply the zero point correction (calculated with BSSE!). > > Of course, I fully agree that BSSE is crucial, especially in ab initio > calculation with small basis set, like MP2/6-31G here. (By the way, > this basis is clearly too small for MP2!) But I have never calculated > zero-point correction with BSSE included: i.e., frequency calculations > for A with dummy atoms on B instead of "normal" frequency calculations > for A. Do you have any experience and comparison, suggesting that not > including dummy atoms in frequency calculations is really important > (i.e., producing an energy difference larger than ~0.1 kcal/mol)? > > Kind regards, > Mariusz Radon > > > > On Wed, Sep 26, 2012 at 8:29 PM, Bradley Welch bwelch5(!)slu.edu > wrote: > > Before anything else I would highly consider doing a BSSE computation. > The > > pople basis sets are prone to significant BSSE. > > > > So what I would do if I had the resources is redo your calculation with > the > > BSSE correction. To get the A-B interaction you would do the following > > > > > > AB= (AB+zp) - ((A+zp) +(B+zp)) > > > > On Tue, Sep 25, 2012 at 11:17 PM, shekhar mittal sumitmittal49 a > gmail.com > > wrote: > >> > >> > >> Sent to CCL by: "shekhar mittal" [sumitmittal49(_)gmail.com] > >> Hi, > >> It is a bit trivial problem but I am quite stuck with it. I have > performed > >> ab initio calculations for a complex (A-B) and its components (A and B) > at > >> the MP2/6-31G level of theory. In the output file, I get energy for each > >> molecule listed as E(MP2). From frequency calculations, I got zero-point > >> corrections. > >> So my question is that while calculating interaction (or stabilization) > >> energy, we use De (i.e. E(MP2)) or Do( E(MP2)-zero point energy > correction)?>> E-mail to subscribers: CHEMISTRY]![ccl.net or use:>> > >> E-mail to administrators: CHEMISTRY-REQUEST]![ccl.net or use>> > >> > > > > > > > > -- > > Bradley Welch > > Saint Louis University > > Monsanto Hall Room 218> > > -- Bradley Welch Saint Louis University Monsanto Hall Room 218 --20cf307ca386adec3e04cac53046 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Mariusz,

I think you're right actually. Thermodynamics probabl= y would not be that sensitive to a slight change in total energy due to the= bsse calculation. My first thought when I saw=A0 his question was treat ev= erything the same. If you do a bsse for one part you do a bsse for the enti= re set of calculations, including your frequency calculations. That though = process itself is probably a beginners mistake.



On Fri, Sep 28, 2012 at 5:55 AM, Mar= iusz Radon mariusz.radon]^[gmail.com <owner-chemistry{:}ccl.net> wrote:

Sent to CCL by: Mariusz Radon [mariusz.radon^_^gmail.com]
Dear CCLers,
let me join this thread and ask a question, addressed mostly to Bradley:
On Wed, Sep 26, 2012 at 8:29 PM, Bradley Welch bwelch5(!)slu.edu
<owner-chemistry%ccl.net> wrote:
> Before anything else I would highly consider doing a BSSE computation.= The
> pople basis sets are prone to significant BSSE.
> (...)
> Then apply the zero point correction (calculated with BSSE!).

Of course, I fully agree that BSSE is crucial, especially in ab initio
calculation with small basis set, like MP2/6-31G here. (By the way,
this basis is clearly too small for MP2!) =A0But I have never calculated zero-point correction with BSSE included: i.e., frequency calculations
for A with dummy atoms on B instead of "normal" frequency calcula= tions
for A. Do you have any experience and comparison, suggesting that not
including dummy atoms in frequency calculations is really important
(i.e., producing an energy difference larger than ~0.1 kcal/mol)?

Kind regards,
Mariusz Radon



On Wed, Sep 26, 2012 at 8:29 PM, Bradley Welch bwelch5(!)slu.edu
<owner-chemistry%ccl.net> wrote:
> Before anything else I would highly consider doing a BSSE computation.= The
> pople basis sets are prone to significant BSSE.
>
> So what I would do if I had the resources is redo your calculation wit= h the
> BSSE correction. =A0To get the A-B interaction you would do the follow= ing
>
>
> AB=3D (AB+zp) - ((A+zp) +(B+zp))
>
> On Tue, Sep 25, 2012 at 11:17 PM, shekhar mittal sumitmittal49 a gmail.com
> <owner-chemistry]![ccl= .net> wrote:
>>
>>
>> Sent to CCL by: "shekhar =A0mittal" [sumitmittal49(_)gmail.com]
>> Hi,
>> It is a bit trivial problem but I am quite stuck with it. I have p= erformed
>> ab initio calculations for a complex (A-B) and its components (A a= nd B) at
>> the MP2/6-31G level of theory. In the output file, I get energy fo= r each
>> molecule listed as E(MP2). From frequency calculations, I got zero= -point
>> corrections.
>> So my question is that while calculating interaction (or stabiliza= tion)
>> energy, we use De (i.e. E(MP2)) or Do( E(MP2)-zero point energy co= rrection)?>> E-mail to subscribers: CHEMISTRY]![ccl.net or use:>>
>> E-mail to administrators: CHEMISTRY-REQUEST]![ccl.net or use>>
>>
>
>
>
> --
> Bradley Welch
> Saint Louis University
> Monsanto Hall Room 218
>



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--
Bradley Welch
Saint= Louis University
Monsanto Hall Room 218

--20cf307ca386adec3e04cac53046-- From owner-chemistry@ccl.net Fri Sep 28 17:20:00 2012 From: "Deepak Bandyopadhyay debug22^-^gmail.com" To: CCL Subject: CCL: call for abstracts: ACS New Orleans session on visualizing/analysing screening data Message-Id: <-47689-120928162022-25597-tQhlV0G4U8YjCAzABbsooA__server.ccl.net> X-Original-From: Deepak Bandyopadhyay Content-Type: multipart/alternative; boundary=f46d044403a084186304cac8c884 Date: Fri, 28 Sep 2012 16:20:13 -0400 MIME-Version: 1.0 Sent to CCL by: Deepak Bandyopadhyay [debug22%gmail.com] --f46d044403a084186304cac8c884 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hello all, I'm chairing a CINF session at the next ACS (New Orleans, April 7-11 2013) on: *=93Advances in Visualizing and Analyzing Biomolecular Screening Data"* If you have a cool new method to enable the rapid visualization and analysis of large amounts of screening data (experimental, not computational vHTS) to find novel hits and/or mine useful and hidden information from screens, and are able to attend this meeting, please submit an abstract for this symposium ASAP. The submission deadline is in mid-Oct. Contact me with any questions. Thanks, Deepak. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Deepak Bandyopadhyay, PhD Principal Scientist, GlaxoSmithKline 1250 S Collegeville Rd, Collegeville PA 19426 Phone: (610) 917 7928 Fax: (610) 917 7393 --f46d044403a084186304cac8c884 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hello all,

I'm chairing a=A0CINF session=A0at the next ACS (New Orleans, April 7-11 2013) on:
= =93Advances in Visualizing and Analyzing Biomolecular Screening Data"
If you have a cool n= ew method to enable the rapid visualization and analysis of large amounts o= f screening data (experimental, not computational vHTS) to find novel hits = and/or mine useful and hidden information from screens, and are able to att= end this meeting, please submit an abstract for this symposium ASAP. The su= bmission deadline is in mid-Oct. Contact me with any questions.

Thanks,
Deepak.
~~~~~~~~~~~~= ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Deepak Bandyopadhyay, PhD=A0 =A0 =A0 = =A0 =A0
Principal Scientist, GlaxoSmithKline
1250 S Collegeville Rd,= Collegeville PA 19426
Phone: (610) 917 7928=A0 =A0 Fax: (610) 917 7393
--f46d044403a084186304cac8c884--