From owner-chemistry@ccl.net Wed Nov 3 07:54:01 2010 From: "partha biswas partha361 . gmail.com" To: CCL Subject: CCL: BSSE calculation m06 level in NWChem Message-Id: <-43058-101102235424-29892-IHVngzbU4JVZXOCmxO0efg^_^server.ccl.net> X-Original-From: "partha biswas" Date: Tue, 2 Nov 2010 23:54:22 -0400 Sent to CCL by: "partha biswas" [partha361|,|gmail.com] Can anyone tell me how to do bsse calculation in M06 level using NWCHem software? Kindly tell how to put an input. From owner-chemistry@ccl.net Wed Nov 3 08:29:01 2010 From: "Jan Labanowski janl]=[speakeasy.net" To: CCL Subject: CCL: CCL may be down for a while Message-Id: <-43059-101103081701-16210-uA6x8AHIyhTggIoGkQQnkA^^^server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 03 Nov 2010 08:08:55 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl=speakeasy.net] Dear CCL Members, I am upgrading power in my house and most likely, sometime before noon NY Time, the power will be out for a few hours. Bear with me. There will be a repeat of the situation in a few days when a new external connection is being made. So, in short, "expect the unexpected" and have patience with me. Jan The CCL Admin From owner-chemistry@ccl.net Wed Nov 3 10:22:01 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek#few.vu.nl" To: CCL Subject: CCL: BSSE calculation m06 level in NWChem Message-Id: <-43060-101103091455-19965-bCaPOzjGcSYG1m6pFbl7xg{=}server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 3 Nov 2010 14:14:48 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek!^!few.vu.nl] > Can anyone tell me how to do bsse calculation in M06 level using NWCHem > software? Kindly tell how to put an input. Just a comment: for M06 the integration grid is quite important so you have to look into that as well (something like "grid superposition error"). I know this is not what you asked for, sorry if you already knew about it. Sincerely, Ulf Ekstrom From owner-chemistry@ccl.net Wed Nov 3 17:37:00 2010 From: "Van Dam, Hubertus J HubertusJJ.vanDam*o*pnl.gov" To: CCL Subject: CCL: BSSE calculation m06 level in NWChem Message-Id: <-43063-101103111339-25552-XOYzn2BUDihPoRfydZMTvg[#]server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 3 Nov 2010 08:13:30 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam||pnl.gov] Hi Partha, The idea of BSSE calculations is that you eliminate the effect the mathematical representation of your problem has on your answers. Given that with localized basis sets the mathematical representation depends on where your atoms are. In order to eliminate that fact you would do the following (I am giving the example for a dimer because that is simple, if you are looking at something else that you need help with, please tell me what it is). Step 1: Do the calculation for the dimer with atoms A and B as you usually would Step 2: Take the input from step 1 and replace atom A with a Bq center but place the same basis set at the Bq center that atom A would have had and do the calculation Step 3: Take the input from step 1 and replace atom B with a Bq center but place the same basis set at the Bq center that atom B would have had and do the calculation Step 4: Take the result from step 1 and subtract the results from step 2 and 3 to get the BSSE free bond energy. If you want to know how to set up the calculations for step 2 and 3, please have a look at the QA test cases in NWChem. In particular the test case dft_bsse (look for the dft_bsse.nw file) should give you a good idea of how to do this. Best wishes, Huub -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnl.gov*_*ccl.net [mailto:owner-chemistry+hubertus.vandam==pnl.gov*_*ccl.net] On Behalf Of partha biswas partha361 . gmail.com Sent: Tuesday, November 02, 2010 8:54 PM To: Van Dam, Hubertus J Subject: CCL: BSSE calculation m06 level in NWChem Sent to CCL by: "partha biswas" [partha361|,|gmail.com] Can anyone tell me how to do bsse calculation in M06 level using NWCHem software? Kindly tell how to put an input.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Nov 3 18:12:01 2010 From: "A VM fray.gory__gmail.com" To: CCL Subject: CCL:G: BSSE energy difference in G03 and NWChem Message-Id: <-43064-101103180152-2866-n+Ozm/18DBLnSHt+qIhqcg#server.ccl.net> X-Original-From: A VM Content-Type: multipart/alternative; boundary=0016367fa440f5d71704942bc767 Date: Wed, 3 Nov 2010 16:21:06 -0400 MIME-Version: 1.0 Sent to CCL by: A VM [fray.gory * gmail.com] --0016367fa440f5d71704942bc767 Content-Type: text/plain; charset=ISO-8859-1 Sir partha biswas, In this nwchem input you are not computing a M05-2x calculation, Alvaro On Tue, Nov 2, 2010 at 4:21 AM, partha biswas partha361###gmail.com < owner-chemistry(~)ccl.net> wrote: > > Sent to CCL by: "partha biswas" [partha361]^[gmail.com] > Sir, > > I have ran the BSSE calculation for water-ammonia cluster in NWCHem as well > as in Gaussian03.I have used the dft method m05-2x/6-31g as the basis set. > Both the jobs ran successfully with following results: > > In NWChem > > BSSE Error= 0.001774669 > Corrected energy = -132.89948836 > In Gaussian > > BSSE energy = 0.00165022 > Corrected energy = -132.89804157 > > My concern is that the corrected energies values differ by a value of > 3KJ/Mol(0.9kcal/mol) whereas the BSSE errors differ by > 0.32kJ/mol(0.077kcal/mol). > So what is the reason for huge difference in corrected energies ..!!. > Moreover I have ran the BSSE Calculation in NWchem and Gaussian03 with HF > method also.There i have found the results quite similar in Gaussian and > NWChem. > > In NWChem(HF/6-31g) > > BSSE Error= 0.001387039 > Corrected energy = -132.162177794 > In Gaussian03(HF/6-31g) > > BSSE Error= 0.0013870449 > Corrected energy = -132.162177768 > > Please see this input file for NWChem > > > scratch_dir /scratch > > title "waterammonia bsse calc " > > start waterammonia > > ##memory global 1024 mb stack 2048 mb heap 2048 mb > > geometry > O -1.54122800 -0.09769000 0.00050800 > H -0.58500900 -0.00294800 -0.00853800 > H -1.98167500 0.74227700 -0.00278600 > N 1.41171900 0.01749500 -0.00026300 > H 1.58776600 -0.46249000 0.85508000 > H 1.83081200 0.92026600 -0.03925000 > H 1.59589900 -0.53804600 -0.80673200 > > end > > basis "ao basis" spherical > O library 6-31g > H library 6-31g > N library 6-31g > bqO library O 6-31g > bqH library H 6-31g > bqN library N 6-31g > end > > driver > clear > end > > bsse > mon water 1 2 3 > mon ammonia 4 5 6 7 > end > > task scf optimize> > > --0016367fa440f5d71704942bc767 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Sir partha biswas,

In this nwchem input = you are not computing a M05-2x calculation,

Alvaro=



On Tue, = Nov 2, 2010 at 4:21 AM, partha biswas partha361###gmail.com <owner-chemistry(~)ccl.net> wrote:

Sent to CCL by: "partha =A0biswas" [partha361]^[gmail.com]
Sir,

I have ran the BSSE calculation for water-ammonia cluster in NWCHem as well=
as in Gaussian03.I have used the dft method m05-2x/6-31g as the basis set.<= br> Both the jobs ran successfully with following results:

In NWChem

BSSE Error=3D 0.001774669
Corrected energy =3D -132.89948836
In Gaussian

BSSE energy =3D 0.00165022
Corrected energy =3D -132.89804157

My concern is that the corrected energies values differ by a value of
3KJ/Mol(0.9kcal/mol) whereas the BSSE errors differ by
0.32kJ/mol(0.077kcal/mol).
So what is the reason for huge difference in corrected energies ..!!.
Moreover I have ran the BSSE Calculation in NWchem and Gaussian03 with HF method also.There i have found the results quite similar in Gaussian and NWChem.

In NWChem(HF/6-31g)

BSSE Error=3D 0.001387039
Corrected energy =3D -132.162177794
In Gaussian03(HF/6-31g)

BSSE Error=3D 0.0013870449
Corrected energy =3D -132.162177768

Please see this input file for NWChem


scratch_dir /scratch

title "waterammonia bsse calc "

start waterammonia

##memory global 1024 mb stack 2048 mb heap 2048 mb

geometry
=A0O =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -1.54122800 =A0 -0.09769000 =A0 =A00.0= 0050800
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -0.58500900 =A0 -0.00294800 =A0 -0.008= 53800
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -1.98167500 =A0 =A00.74227700 =A0 -0.0= 0278600
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01.41171900 =A0 =A00.01749500 =A0 -0= .00026300
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01.58776600 =A0 -0.46249000 =A0 =A00= .85508000
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01.83081200 =A0 =A00.92026600 =A0 -0= .03925000
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01.59589900 =A0 -0.53804600 =A0 -0.8= 0673200

end

basis "ao basis" spherical
=A0O library 6-31g
=A0H library 6-31g
=A0N library 6-31g
=A0bqO library O 6-31g
=A0bqH library H 6-31g
=A0bqN library N 6-31g
end

driver
=A0clear
end

bsse
=A0mon =A0water 1 2 3
=A0mon ammonia 4 5 6 7
end

task scf optimize



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY(~)ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST(~)ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--0016367fa440f5d71704942bc767-- From owner-chemistry@ccl.net Wed Nov 3 20:14:01 2010 From: "Jun Zhang coolrainbow^^yahoo.cn" To: CCL Subject: CCL: question on Born-Oppenheimer approx. Message-Id: <-43065-101103200951-25716-rqHyMoF11oPF6LdbF5wy0Q-$-server.ccl.net> X-Original-From: Jun Zhang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Thu, 4 Nov 2010 08:09:41 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow-*-yahoo.cn] Hi everyone: This question is quite fundermental. I share the somewhat similar opinion with Ulf Ekstrom. For an isolate molecule in vacuo, by time-independent SE beyond the BO approximation with bound state condition, e.g. CH3OCH3 and C2H5OH, they of ourse have the same form of SE and have the same solutions. BO approximation, although excellent, does not tell us why a particular nuclear configuration can be stable (geometry optimization is not the answer since the conception of PES is within the framework of BO). In my opinion, the introduction of BO approximation can be viewed as a "coarse grain" decription of the molecule world, i.e. "unknown" of the history of the molecule or the rest of the world. The stable existence of a specific configuration, CH3OCH3 or C2H5OH, might be traced back to a particular initial condition at time t=t0, which has made the solution of SE might have some special dynamics properties that the time evolution of the configuration is very slow. Another possibility is that the condense state of material might stabilize the molecule, or we may say that it is those molecular configurations which can "survive" or "be robust" in the environmant are able to be stationary, or as Ulf Ekstrom stated, "pointer state". BO approximation that fixes a known nuclear configuration, in my point of view, is the reduced description of all other "unknowns" Jun Zhang Nankai University coolrainbow---yahoo.cn From owner-chemistry@ccl.net Wed Nov 3 23:25:00 2010 From: "Henry Martinez hmartine^gmail.com" To: CCL Subject: CCL: Potential energy scan and Transition state Message-Id: <-43066-101103231623-26445-6rBfkp2BdCzEAA8riZFAJQ_-_server.ccl.net> X-Original-From: "Henry Martinez" Date: Wed, 3 Nov 2010 23:16:22 -0400 Sent to CCL by: "Henry Martinez" [hmartine+*+gmail.com] I would like to do a potential energy scan (PES) with a Transition State (TS) at the same time. I mean, when the scan gets to the correct distance where the transition state happens I would like it to be calculated. Is that possible? If so, how the input should looks like? Anybody could give me an example with a simple SN2 reaction? Thanks a lot for the help.