From owner-chemistry@ccl.net Mon Nov 28 00:14:00 2011 From: "Pezhman Zarabadip-Poor pzarabadip~!~gmail.com" To: CCL Subject: CCL: Suitable Basis set for Hg(II) Calculation Message-Id: <-45932-111128000932-13713-Qda366XXAoDy4vYlBWwkIA!A!server.ccl.net> X-Original-From: "Pezhman Zarabadip-Poor" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 28 Nov 2011 08:39:13 +0330 MIME-Version: 1.0 Sent to CCL by: "Pezhman Zarabadip-Poor" [pzarabadip ~ gmail.com] Dear Ted, I have not employed mentioned Stuttgart basis sets yet. I think I should try them and evaluate the results. Until now I used LANL2DZ, aug-cc-pVDZ--->QZ, and def2-TZVP basis sets. The starting point of these calculations is based on a published paper in which the authors used LANL2DZ for Hg(II) ions and claimed that these ions coordinate to two oxygen atoms of sulfonic acid groups of the main molecule. According to the nature of this interaction which is electrostatic one between Hg(2+) and one negatively charged oxygen I guessed that maybe this proposed structure is not correct. Then, I checked the structure with other basis sets and obtained the structure which I expected (Hg(2+) is in interaction with one oxygen atom on each sulfonic acid group). Then, I came to this point that is my guess and consequent conclusion is correct or the used basis set was not suitable for this system and brought me to a expected point but on a wrong way?! I think maybe I should try LANL2TZ and check the results too?! Best regards, Pezhman -----Original Message----- > From: owner-chemistry+pzarabadip==gmail.com%%ccl.net [mailto:owner-chemistry+pzarabadip==gmail.com%%ccl.net] On Behalf Of Theodore S. Dibble tsdibble*o*esf.edu Sent: Monday, November 28, 2011 5:42 AM To: Zarabadi-Poor, Pezhman Subject: CCL: Suitable Basis set for Hg(II) Calculation Sent to CCL by: "Theodore S. Dibble" [tsdibble##esf.edu] Pezhman, In general, one expects the LANL2DZ basis set is far surpassed by the Stuttgart basis sets, available at http://www.theochem.uni-stuttgart.de/pseudopotentials/index.en.html. This site provides ECPs and matching correlation-consistent basis sets for the outer electrons. It is certainly possible that LANL2DZ actually performs better than more recent basis sets for certain classes of problems. Are there experimental data sets you can use to validate your methods? Best wishes, Ted Dibble Theodore S. Dibble Professor of Chemistry SUNY-Environmental Science and Forestry 1 Forestry Drive Syracuse, NY 13210 (315) 470-6596 (315) 470-6856 (fax) http://www.esf.edu/chemistry/faculty/dibble.htm > "Pezhman Zarabadi-Poor pzarabadip]~[gmail.com" wrote: > > Sent to CCL by: "Pezhman Zarabadi-Poor" [pzarabadip/a\gmail.com] > Dear CCL users, > > I am planning to do some DFT and TDDFT calculations on a complex of Hg(II) and > a naphthalene sulfonic acid derivative. I searched through the literature and > found that some of previous computational works have employed ECP-LANL2DZ for > Hg(II). Is it a good suggestion for doing such calculations? I checked the > larger basis sets such as aug-cc-pVDZ to QZ but I obtained a little bit > different results than the published ones? According to the consultant with an > expert person, there is guess that maybe employing larger basis sets makes Hg > ions too soft and makes the results wrong! > > Your suggestions about the appropriate method/basis sets are highly > appreciated. > > Best regards, > Pezhman Zarabadi-Poorhttp://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 Mon Nov 28 08:09:01 2011 From: "partha kundu partha1kundu%a%gmail.com" To: CCL Subject: CCL: optimization problem Message-Id: <-45933-111128014907-4878-++WUUbFq+TBCYyXTIq1BFg]|[server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary=0015175ce0f6b8ae2304b2c5e562 Date: Mon, 28 Nov 2011 12:18:18 +0530 MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu-*-gmail.com] --0015175ce0f6b8ae2304b2c5e562 Content-Type: text/plain; charset=ISO-8859-1 Dear Dr. Catherine, I tried all your methods but nothing worked. When I replaced Cd with Cr it did not show any error (although it did not converge, may be due to other issue). So it seems the problem is not with the empty line or ****. Also my latest input is as follows: %chk=a.chk %nproc=4 %mem=60MW #p b3lyp/gen pseudo=read opt counterpoise=5 title 0 1 -4 1 1 1 1 1 1 1 1 1 Cd(Fragment=1) 0.03610900 -0.05624800 -0.0490050 Cl(Fragment=1) 2.33192200 -1.18838500 0.9159510 Cl(Fragment=1) 1.11114500 2.62546300 0.0654750 . . . . . H(Fragment=5) 0.37163500 -3.55841500 5.4056200 C N Cl H 0 6-31+G(d) **** Cd 0 LANL2DZ **** Cd LANL2DZ It is converging with the Warning message: Warning! Cd atom 1 has 48 valence electrons but only 18 basis functions. Also about assigning the charge of each fragment it is saying: Sum of Mulliken charges with hydrogens summed into heavy atoms = 1.00000 Condensed to fragments (all electrons): 1 0.000523 2 0.001234 3 -0.000166 4 -0.000022 5 0.998431 Kindly help. regards. Partha P. Kundu PhD student Light Scattering Laboratory Chemistry & Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, 560064 INDIA Phone +91 80 2208 2811/2853 (Lab) On Thu, Nov 24, 2011 at 1:25 PM, Esterhuysen, Catharine, Dr < ce-$-sun.ac.za> wrote: > ** > Hi! > > I've sometimes had this kind of problem and often this has to do with > empty lines and/or asterisks when giving the Gen basis set at the end. Play > with taking out the asterisks at the end of the basis set definition and if > that doesn't work try omitting the open line between basis set definition > and ecp definition. > > Good luck! > > Catharine > > ------------------------------ > *From:* owner-chemistry+ce==sun.ac.za-$-ccl.net [mailto:owner-chemistry+ce== > sun.ac.za-$-ccl.net] *On Behalf Of *partha kundu partha1kundu/./gmail.com > *Sent:* 23 November 2011 02:42 PM > *To:* Esterhuysen, Catharine, Dr > *Subject:* CCL: optimization problem > > > Sorry, > My message was incomplete. > it should be > I am trying to optimize a structure using counterpoise keyword to assign > different charge and spin for different fragment. My input is like: > %chk=cd.chk > %mem=200MW > %nproc=4 > # b3lyp/gen pseudo=read opt counterpoise=2 > > Title Card Required > > 0,1 -4,1 4,1 > Cd 0.03610900 -0.05624800 -0.04900500 1 > Cl 2.33192200 -1.18838500 0.91595100 1 > . > . > . > . > H 0.37163500 -3.55841500 5.40562000 2 > > C N H 0 > STO-3G > **** > Cl 0 > 3-21G > **** > Cd 0 > LANL2DZ > **** > > Cd 0 > LANL2DZ > > > Output is saying: > > Warning! Cd atom 1 has 48 valence electrons but only 18 basis > functions. > > This is less than a minimal basis set! > > Also the mulliken charge I am getting is sometimes 4,0,-4. > > I would appreciate any help resolving the problem. > > With kind regards. > > Partha. > > > > > > > > > On Wed, Nov 23, 2011 at 4:48 PM, Partha Kundu partha1kundu,gmail.com < > owner-chemistry,ccl.net> wrote: > >> >> Sent to CCL by: "Partha Kundu" [partha1kundu[-]gmail.com] >> Dear All, >> I am trying to optimize a structure using counterpoise keyword to assign >> different charge and spin for different fragment. My input is like: >> %chk=cd.chk >> %mem=200MW >> %nproc=4 >> # b3lyp/gen pseudo=read scf=(tight,maxcycle=1000)counterpoise=2 opt >> >> Title Card Required >> >> 0,1 -4,1 4,1 >> Cd 0.03610900 -0.05624800 -0.04900500 1 >> Cl 2.33192200 -1.18838500 0.91595100 1** >> E-mail to subscribers: CHEMISTRY,ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST,ccl.net or use>> **>> >> >> > --0015175ce0f6b8ae2304b2c5e562 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Dr. Catherine,
I tried all your methods but nothing worked. When I = replaced Cd with Cr it did not show any error (although it did not converge= , may be due to other issue). So it seems the problem is not with the empty= line or ****. Also my latest input is as follows:
%chk=3Da.chk
%nproc=3D4
%mem=3D60MW
#p b3lyp/gen pseudo=3Dread op= t counterpoise=3D5

title

0 1 -4 1 1 1 1 1 1 1 1 1
=A0Cd(F= ragment=3D1)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.03610900=A0=A0 -0.056248= 00=A0=A0 -0.0490050=A0
=A0Cl(Fragment=3D1)=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 2.33192200=A0=A0 -1.18838500=A0=A0=A0 0.9159510=A0
=A0Cl(Fragment=3D1)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.11114500=A0=A0=A0= 2.62546300=A0=A0=A0 0.0654750=A0
.
.
.
.
.
=A0
=A0H= (Fragment=3D5)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.37163500=A0=A0 -3.5= 5841500=A0=A0=A0 5.4056200

C N Cl H 0
6-31+G(d)
****
Cd 0<= br>LANL2DZ
****

Cd
LANL2DZ

It is converging with the Warning message= :
Warning!=A0 Cd atom=A0=A0=A0 1 has 48 valence electrons but only=A0 18 basis functions.

Also about assigning the charge of each fragment it is saying:

Sum of Mulliken charges with hydrogens summed into heavy atoms =3D=A0=A0 <= /span>1.00000

=A0=A0=A0=A0=A0=A0=A0=A0=A0 Condensed to fragm= ents (all electrons):

=A0=A0=A0=A0 1=A0=A0=A0=A0=A0= =A0 0.000523

=A0=A0=A0=A0 2=A0=A0=A0=A0=A0= =A0 0.001234

=A0=A0=A0=A0 3=A0=A0=A0=A0=A0 -0.000166

=A0=A0=A0=A0 4=A0=A0=A0=A0=A0 -0.000022

=A0=A0=A0=A0 5=A0=A0=A0=A0=A0= =A0 0.998431

Kindly help.
regards.


Partha P. Kundu
PhD s= tudent
Light Scattering Laboratory
Chemistry & Physics of Materi= als Unit
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCAS= R), Bangalore,=A0 560064 INDIA
Phone +91 80 2208 2811/2853 (Lab)


On Thu, Nov 24, 2011 at 1:25 PM, Esterhu= ysen, Catharine, Dr <ce-$-sun.ac.za>= ; <ce-$-sun.ac.za>= ; wrote:
Hi!
=A0
I've sometimes had this kind of problem and often this=20 has to do with empty lines and/or asterisks when giving the Gen basis set a= t the=20 end. Play with taking out the asterisks at the end of the basis set definit= ion=20 and if that doesn't work try omitting the open line between basis set d= efinition=20 and ecp definition.
=A0
Good luck!
=A0
Catharine

From: owner-chemistry+ce=3D=3Dsun.ac.za-$-ccl.net=20 [mailto:owner-che= mistry+ce=3D=3Ds= un.ac.za-$-ccl.net] On Behalf Of partha kundu=20 partha1kundu/./gmail.com=
Sent: 23 November 2011 02:42 PM
To:=20 Esterhuysen, Catharine, Dr <ce-$-sun.ac.za>
Subject: CCL:=20 optimization problem


Sorry,
My message was incomplete.
it sho= uld=20 be
I am trying to optimize a structure using counterpoise keyword to ass= ign=20 different charge and spin for different fragment. My input is like:
%chk=3Dcd.chk
%mem=3D200MW
%nproc=3D4
# b3lyp/gen pseudo=3Dre= ad opt=20 counterpoise=3D2

Title Card Required

0,1 -4,1=20 4,1
=A0Cd=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=20 0.03610900=A0=A0 -0.05624800=A0=A0 -0.04900500=20 1
=A0Cl=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=20 2.33192200=A0=A0 -1.18838500=A0=A0=A0 0.91595100=20 1
=A0.
.
.
.
=A0H=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=20 0.37163500=A0=A0 -3.55841500=A0=A0=A0 5.40562000 2

C N H=20 0
STO-3G
****
Cl 0
3-21G
****
Cd=20 0
LANL2DZ
****

Cd 0
LANL2DZ


Output is saying:

Warning!=A0 Cd=20 atom=A0=A0=A0 1 has 48 valence electrons but=20 only=A0 18 basis functions.

=A0This= is less than a=20 minimal basis set!

Also the mulliken=20 charge I am getting is sometimes 4,0,-4.

I would=20 appreciate any help resolving the problem.

With kind=20 regards.

Partha.



=A0





On Wed, Nov 23, 2011 at 4:48 PM, Partha Kundu=20 partha1kundu,gmail.com <= span dir=3D"ltr"><owner-chemistry,ccl.net>=20 wrote:

Sent to CCL b= y: "Partha =A0Kundu" [partha1kundu[-]gmail.com]
Dear All,
I am=20 trying to optimize a structure using counterpoise keyword to assign diffe= rent=20 charge and spin for different fragment. My input is=20 like:
%chk=3Dcd.chk
%mem=3D200MW
%nproc=3D4
# b3lyp/gen pseud= o=3Dread=20 scf=3D(tight,maxcycle=3D1000)counterpoise=3D2 opt

Title Card=20 Required

0,1 -4,1 4,1
=A0Cd =A0 =A0 =A0 =A0 =A0=20 =A0 =A0 =A0 0.03610900 =A0 -0.05624800 =A0 -0.04900500=20 1
=A0Cl =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=20 2.33192200 =A0 -1.18838500 =A0 =A00.91595100 1



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--0015175ce0f6b8ae2304b2c5e562-- From owner-chemistry@ccl.net Mon Nov 28 08:44:01 2011 From: "Mark Iron Mark.A.Iron=-=weizmann.ac.il" To: CCL Subject: CCL: Suitable Basis set for Hg(II) Calculation Message-Id: <-45934-111128020746-11822-H91gOnr8z7iJOdVkum2sQQ%a%server.ccl.net> X-Original-From: Mark Iron Content-Language: en-CA Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 28 Nov 2011 07:07:34 +0000 MIME-Version: 1.0 Sent to CCL by: Mark Iron [Mark.A.Iron * weizmann.ac.il] Dear all, Another basis set one could try are Prof. Peterson's cc-pVnZ-PP basis sets (and their augmented versions). I have used them a fair bit with satisfactory results (albeit not yet for Hg) and they are designed to be used with the standard Dunning cc-pVnZ basis sets on the main-group elements. This set allows one to increase basis set size from double-zeta through quintuple-zeta (for the bold at heart). These, and many others, as always are available from the EMSL Basis Set Library in a wide variety of formats: https://bse.pnl.gov/bse/portal I hope this helps. Mark. ________________________________ Dr. Mark Iron, Computational Chemistry Unit, Department of Chemical Research Support, Kimmelman 251, Weizmann Institute of Science, Rehovot, Israel 76100. Tel: +972 8 934 6218 Fax: +972 8 934 4142 e-mail: mark.a.iron .. weizmann.ac.il web: http://compchem.weizmann.ac.il/ccu/ No trees were killed in the sending of this message. However, a large number of electrons were terribly inconvenienced. ________________________________________ > From: owner-chemistry+mark.a.iron==weizmann.ac.il .. ccl.net [owner-chemistry+mark.a.iron==weizmann.ac.il .. ccl.net] on behalf of Pezhman Zarabadip-Poor pzarabadip~!~gmail.com [owner-chemistry .. ccl.net] Sent: November 28, 2011 7:09 AM To: Mark Iron Subject: CCL: Suitable Basis set for Hg(II) Calculation Sent to CCL by: "Pezhman Zarabadip-Poor" [pzarabadip ~ gmail.com] Dear Ted, I have not employed mentioned Stuttgart basis sets yet. I think I should try them and evaluate the results. Until now I used LANL2DZ, aug-cc-pVDZ--->QZ, and def2-TZVP basis sets. The starting point of these calculations is based on a published paper in which the authors used LANL2DZ for Hg(II) ions and claimed that these ions coordinate to two oxygen atoms of sulfonic acid groups of the main molecule. According to the nature of this interaction which is electrostatic one between Hg(2+) and one negatively charged oxygen I guessed that maybe this proposed structure is not correct. Then, I checked the structure with other basis sets and obtained the structure which I expected (Hg(2+) is in interaction with one oxygen atom on each sulfonic acid group). Then, I came to this point that is my guess and consequent conclusion is correct or the used basis set was not suitable for this system and brought me to a expected point but on a wrong way?! I think maybe I should try LANL2TZ and check the results too?! Best regards, Pezhman -----Original Message----- > From: owner-chemistry+pzarabadip==gmail.com]~[ccl.net [mailto:owner-chemistry+pzarabadip==gmail.com]~[ccl.net] On Behalf Of Theodore S. Dibble tsdibble*o*esf.edu Sent: Monday, November 28, 2011 5:42 AM To: Zarabadi-Poor, Pezhman Subject: CCL: Suitable Basis set for Hg(II) Calculation Sent to CCL by: "Theodore S. Dibble" [tsdibble##esf.edu] Pezhman, In general, one expects the LANL2DZ basis set is far surpassed by the Stuttgart basis sets, available at http://www.theochem.uni-stuttgart.de/pseudopotentials/index.en.html. This site provides ECPs and matching correlation-consistent basis sets for the outer electrons. It is certainly possible that LANL2DZ actually performs better than more recent basis sets for certain classes of problems. Are there experimental data sets you can use to validate your methods? Best wishes, Ted Dibble Theodore S. Dibble Professor of Chemistry SUNY-Environmental Science and Forestry 1 Forestry Drive Syracuse, NY 13210 (315) 470-6596 (315) 470-6856 (fax) http://www.esf.edu/chemistry/faculty/dibble.htm > "Pezhman Zarabadi-Poor pzarabadip]~[gmail.com" wrote: > > Sent to CCL by: "Pezhman Zarabadi-Poor" [pzarabadip/a\gmail.com] > Dear CCL users, > > I am planning to do some DFT and TDDFT calculations on a complex of Hg(II) and > a naphthalene sulfonic acid derivative. I searched through the literature and > found that some of previous computational works have employed ECP-LANL2DZ for > Hg(II). Is it a good suggestion for doing such calculations? I checked the > larger basis sets such as aug-cc-pVDZ to QZ but I obtained a little bit > different results than the published ones? According to the consultant with an > expert person, there is guess that maybe employing larger basis sets makes Hg > ions too soft and makes the results wrong! > > Your suggestions about the appropriate method/basis sets are highly > appreciated. > > Best regards, > Pezhman Zarabadi-Poorhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://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 Mon Nov 28 09:19:01 2011 From: "Darpan Aulakh darpan.aulakh2011**gmail.com" To: CCL Subject: CCL: query on NEDA Message-Id: <-45935-111127232743-10179-T6FsOQWKflgh2XxN0vk1zQ : server.ccl.net> X-Original-From: Darpan Aulakh Content-Type: multipart/alternative; boundary=f46d0417053b0ce7c904b2c3ec27 Date: Sun, 27 Nov 2011 20:27:35 -0800 MIME-Version: 1.0 Sent to CCL by: Darpan Aulakh [darpan.aulakh2011*o*gmail.com] --f46d0417053b0ce7c904b2c3ec27 Content-Type: text/plain; charset=ISO-8859-1 I want to perform NEDA calculation for water dimer at B3LYP/aug-cc-pvtz level using the B3LYP/aug-cc-pvtz optimized geometry. I have NBO 5.9 running on Gamess. I have performed this calculation using the keyword GBASIS = TZV but the results dont match with the reported ones. Sir please let me know if any other keyword is also to be used??? --f46d0417053b0ce7c904b2c3ec27 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I want to perform NEDA calculation for water dimer at B3LYP/aug-cc-pvtz level using the B3LYP/aug-cc-pvtz optimized geometry.=A0 I have NBO 5.9=20 running on Gamess. I have performed this calculation using the keyword=20 GBASIS =3D TZV but the results dont match with the reported ones. Sir=20 please let me know if any other keyword is also to be used??? --f46d0417053b0ce7c904b2c3ec27-- From owner-chemistry@ccl.net Mon Nov 28 09:54:01 2011 From: "Jean Jules FIFEN julesfifen[*]gmail.com" To: CCL Subject: CCL:G: questions on convergence, restarting jobs, counterpoise Message-Id: <-45936-111128083205-12632-R0uJMP4+b0vJ5UAmDkAhgw * server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 28 Nov 2011 14:31:57 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen*_*gmail.com] Dear Saurabh, 1. For the first questions, you have to know that it is the convention in gaussian implementation that when the forces is to low (less than 5% of the convergence threshold), the obtained geometry is the stationary one whatever the values of the displacement, RMS and so forth. So you do not have to worry about your obtained result. It is good, and further computation are useless. 2. Clearly, I do not understand well your second question. However, you have to keep in mind that restarting frequency jobs could be possible in gaussian09 and not in earlier versions. 3. Can the output of a counterpoise calculation (i.e. the Corrected total energy) be interpreted as a bond-dissociation energy between the two fragments? The answer is no. Counterpoise calculation allows you to encompasse basis set superposition error (BSSE) in your computed energy. Hope this would help. On 27/11/2011, Saurabh S Chitnis sschitnis%x%gmail.com wrote: > > Sent to CCL by: "Saurabh S Chitnis" [sschitnis _ gmail.com] > Hello, > > I have three questions: > > 1. In many of my "opt" and "freq=raman" jobs, I find that the calculation > completes successfully with > the forces having converged but the displacements still being above the > convergence threshold. How > can this be fixed? I usually face this problem when using opt=verytight and > int=ultrafine. > > 2. Is there any way of restarting an analytic frequency job which has > completed but not converged? > > 3. Can the output of a counterpoise calculation (i.e. the Corrected total > energy) be interpreted as a > bond-dissociation energy between the two fragments? > > Here are some details regarding the above questions: > > theory: DFT (B3LYP, PBE1PBE and B3PW91) > > basis-set: cc-pvtz and aug-cc-pvtz > > systems being calcualated: P2Me4, [P2Me5]+ and [P2Me6]2+ > > for the couterpoise: I'm trying to get the P-P bond dissocation energy. So I > optimize the geometry as > per usual and then redefine the optimized P2Me4 as fragment1(Me2P) and > fragment2(PMe2) to run > the counterpoise calculation. The result should be the homolytic bond > dissociation energy right? > > cheers > Saurabh> > > -- Jules. From owner-chemistry@ccl.net Mon Nov 28 10:28:01 2011 From: "Victor Rosas Garcia rosas.victor^gmail.com" To: CCL Subject: CCL: query on NEDA Message-Id: <-45937-111128095135-31359-hEB99NJTILi2NMW/jy0j9Q]_[server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=0016e65a0ca61d3ce704b2cca328 Date: Mon, 28 Nov 2011 08:51:26 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor-,-gmail.com] --0016e65a0ca61d3ce704b2cca328 Content-Type: text/plain; charset=ISO-8859-1 Probably because GBASIS = TZV does not choose aug-cc-pvtz. I think you need to use GBASIS = ACCT for this. Check the manual to be sure. Hope this helps Victor 2011/11/27 Darpan Aulakh darpan.aulakh2011**gmail.com < owner-chemistry:+:ccl.net> > I want to perform NEDA calculation for water dimer at B3LYP/aug-cc-pvtz > level using the B3LYP/aug-cc-pvtz optimized geometry. I have NBO 5.9 > running on Gamess. I have performed this calculation using the keyword > GBASIS = TZV but the results dont match with the reported ones. Sir please > let me know if any other keyword is also to be used??? --0016e65a0ca61d3ce704b2cca328 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Probably because GBASIS =3D TZV does not choose aug-cc-pvtz.=A0 I think you= need to use GBASIS =3D ACCT for this.=A0 Check the manual to be sure.
<= br>Hope this helps

Victor

2011/11/= 27 Darpan Aulakh darpan.aulakh2011**gmail.com<= /a> <owner-= chemistry:+:ccl.net>
I want to perfor= m NEDA calculation for water dimer at B3LYP/aug-cc-pvtz level using the B3LYP/aug-cc-pvtz optimized geometry.=A0 I have NBO 5.9=20 running on Gamess. I have performed this calculation using the keyword=20 GBASIS =3D TZV but the results dont match with the reported ones. Sir=20 please let me know if any other keyword is also to be used???

--0016e65a0ca61d3ce704b2cca328-- From owner-chemistry@ccl.net Mon Nov 28 12:56:01 2011 From: "m.eslamibidgoli]=[mun.ca" To: CCL Subject: CCL: G09_opt 3D PBC_total charge is not ZERO Message-Id: <-45938-111128112012-23888-P783dtCtHRTYqQdqdSvmIg[#]server.ccl.net> X-Original-From: m.eslamibidgoli],[mun.ca Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 28 Nov 2011 12:50:01 -0330 MIME-Version: 1.0 Sent to CCL by: m.eslamibidgoli .. mun.ca Dear CCL Subscribers, I wanted to optimize a polymer structure in a 3D PBC job with G09, containing 138 atoms in the unit cell, using B97D/6-31G(d) level. But after about 10 hours my job was killed with this error: Total Charge is not ZERO/ There is a problem with the total charge; However, the value of the total charge is quite close to zero (ignorable). Would you please help me how I can solve this issue in G09? Is there any possible way to increase the limit value for the total charge? Thanks in advance, Mehrtoos This electronic communication is governed by the terms and conditions at http://www.mun.ca/cc/policies/electronic_communications_disclaimer_2011.php From owner-chemistry@ccl.net Mon Nov 28 14:01:00 2011 From: "Nuno A. G. Bandeira nuno.bandeira---ist.utl.pt" To: CCL Subject: CCL: G09_opt 3D PBC_total charge is not ZERO Message-Id: <-45939-111128135807-24020-1XBgQ1P4ALSzCYXs1TVovg(_)server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Mon, 28 Nov 2011 18:56:29 +0000 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira,+,ist.utl.pt] On 28-11-2011 16:20, m.eslamibidgoli]=[mun.ca wrote: > > I wanted to optimize a polymer structure in a 3D PBC job with G09, containing > 138 atoms in the unit cell, using B97D/6-31G(d) level. But after about 10 hours > my job was killed with this error: Total Charge is not ZERO/ There is a problem > with the total charge; However, the value of the total charge is quite close to > zero (ignorable). Would you please help me how I can solve this issue in G09? Is > there any possible way to increase the limit value for the total charge? > I believe you have a k-point grid problem. Use a wider unit cell range. See http://scuseria.rice.edu/gau/g09_pbc/pbc_guide.html -- Nuno A. G. Bandeira, AMRSC -- From owner-chemistry@ccl.net Mon Nov 28 14:36:01 2011 From: "Vel Murugan G murugan4chemistry^^gmail.com" To: CCL Subject: CCL:G: How To Specify DMF Solvent In Gaussian Input Message-Id: <-45940-111128134912-740-XS9ZZdKgX045BGT2mR9KbA ~~ server.ccl.net> X-Original-From: "Vel Murugan G" Date: Mon, 28 Nov 2011 13:49:07 -0500 Sent to CCL by: "Vel Murugan G" [murugan4chemistry,+,gmail.com] Dear CClers I need to run a PCM calculation with dimethylformamide DMF) as the solvent. I was trying to specify DMF using the PCM model in Gaussian which is not mentioned in the calculation part of the Gauss View. Does anyone know how to specify DMF solvent in Gaussian input? Kindly help me. Thanks in advance With Regards VELMURUGAN G From owner-chemistry@ccl.net Mon Nov 28 16:25:01 2011 From: "P.D.Jarowski-#-surrey.ac.uk" To: CCL Subject: CCL:G: How To Specify DMF Solvent In Gaussian Input Message-Id: <-45941-111128161144-14341-7O3wSFnkpEl1TK1t9Bau2A ~~ server.ccl.net> X-Original-From: Content-Language: en Content-Type: multipart/alternative; boundary="_000_CAF9A9842D35pj0013surreyacuk_" Date: Mon, 28 Nov 2011 21:11:32 +0000 MIME-Version: 1.0 Sent to CCL by: [P.D.Jarowski_._surrey.ac.uk] --_000_CAF9A9842D35pj0013surreyacuk_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, This answer may be annoying, but you could try acetonitrile (SCRF=3D(PCM,CH= 3CN)). I have found that it is a good substitute for DMF. Else, you will ne= ed to collect the solvent parameters for DMF from another program or from t= he literature. Best of Luck Peter On 11/28/11 6:49 PM, "Vel Murugan G murugan4chemistry^^gmail.com" wrote: Sent to CCL by: "Vel Murugan G" [murugan4chemistry,+,gmail.com] Dear CClers I need to run a PCM calculation with dimethylformamide DMF) as the = solvent. I was trying to specify DMF using the PCM model in Gaussian which = is not mentioned in the calculation part of the Gauss View. Does anyone kno= w how to specify DMF solvent in Gaussian input? Kindly help me. Thanks in advance With Regards VELMURUGAN G -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_CAF9A9842D35pj0013surreyacuk_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Re: CCL:G: How To Specify DMF Solvent In Gaussian Input Hi,

This answer may be annoying, but you could try acetonitrile (SCRF=3D(PCM,CH= 3CN)). I have found that it is a good substitute for DMF. Else, you will ne= ed to collect the solvent parameters for DMF from another program or from t= he literature.

Best of Luck

Peter

On 11/28/11 6:49 PM, "Vel Murugan G murugan4chemistry^^gmail.com"= <owner-chemistry|a|ccl.net> wr= ote:



Sent to CCL by: "Vel Murugan G" [murugan4chemistry,+,gmail.com] Dear CClers
        I need to run a PCM calcula= tion with dimethylformamide DMF) as the solvent. I was trying to specify DM= F using the PCM model in Gaussian which is not mentioned in the calculation= part of the Gauss View. Does anyone know how to specify DMF solvent in Gau= ssian input? Kindly help me.

Thanks in advance

With Regards
VELMURUGAN G



-=3D This is automatically added to each message by the mailing script =3D-=
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--_000_CAF9A9842D35pj0013surreyacuk_-- From owner-chemistry@ccl.net Mon Nov 28 17:00:01 2011 From: "Edward Holland hollandej^^^Cardiff.ac.uk" To: CCL Subject: CCL:G: How To Specify DMF Solvent In Gaussian Input Message-Id: <-45942-111128161053-12578-RSfF1FVInX/bKweCTc2DOA() server.ccl.net> X-Original-From: Edward Holland Content-Type: multipart/signed; boundary="Apple-Mail=_D6DA5112-121A-4858-AA81-DD7411CCBDBE"; protocol="application/pgp-signature"; micalg=pgp-sha1 Date: Mon, 28 Nov 2011 21:10:33 +0000 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Edward Holland [hollandej%Cardiff.ac.uk] --Apple-Mail=_D6DA5112-121A-4858-AA81-DD7411CCBDBE Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Hi, http://www.gaussian.com/g_tech/g_ur/k_scrf.htm is the page that lists = all the solvents available. Try using "n,n-DiMethylFormamide" instead of "DMF" Yours Ed Holland On 28 Nov 2011, at 18:49, Vel Murugan G murugan4chemistry^^gmail.com = wrote: >=20 > Sent to CCL by: "Vel Murugan G" [murugan4chemistry,+,gmail.com] > Dear CClers > I need to run a PCM calculation with dimethylformamide DMF) as = the solvent. I was trying to specify DMF using the PCM model in Gaussian = which is not mentioned in the calculation part of the Gauss View. Does = anyone know how to specify DMF solvent in Gaussian input? Kindly help = me. >=20 > Thanks in advance >=20 > With Regards > VELMURUGAN G >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail=_D6DA5112-121A-4858-AA81-DD7411CCBDBE Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename=signature.asc Content-Type: application/pgp-signature; name=signature.asc Content-Description: Message signed with OpenPGP using GPGMail -----BEGIN PGP SIGNATURE----- iQEcBAEBAgAGBQJO0/jJAAoJEEJc9s8gBQlyAw0H/RDG80h1xVfAfvvBVW4RXtu1 qPXhhHj2fUXShrkKqD70sonTlbXRIn3GvCTcOK+JFCti0Pmo+K5UUCSVOj4EPq32 /bhdCpi2sOWC74udeBTva7ajJ41BJzqc32jm3nKcBa+CzDxzcoH/8GkumNNoDPiQ l6jQlmIjVnacTToBIS2EV3UFAYgQWYMSNIL7tMa8pAStxYifpQnXXrNXMOfcGqZf z+cTcEde90VU29mx9H49+AZ3rxNhfEcgVi3zB3Ba/Wzc30mj8fMquv/YiXVVgUSV f+u2ahf4m+ooDRowUFqry9oc4VWWxeYuwhfhHQC443hN1eZ1xOX6OdmUe5gVDZU= =reZq -----END PGP SIGNATURE----- --Apple-Mail=_D6DA5112-121A-4858-AA81-DD7411CCBDBE-- From owner-chemistry@ccl.net Mon Nov 28 21:15:01 2011 From: "Jorge Gancheff jorge~~fq.edu.uy" To: CCL Subject: CCL:G: How To Specify DMF Solvent In Gaussian Input Message-Id: <-45943-111128192255-23225-v6lGafrV6RatJ+nivftnTA*server.ccl.net> X-Original-From: "Jorge Gancheff" Content-Language: en-us Content-Type: multipart/mixed; boundary="----=_NextPart_000_0044_01CCAE1C.394B1140" Date: Mon, 28 Nov 2011 22:22:28 -0200 MIME-Version: 1.0 Sent to CCL by: "Jorge Gancheff" [jorge(a)fq.edu.uy] This is a multi-part message in MIME format. ------=_NextPart_000_0044_01CCAE1C.394B1140 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi, to use N,N-DMF as solvent in PCM calculation in Gaussian, you have to use a non standard input. For this solvent, the appropriate parameters are (include them at the end of your input file): eps=36.71 rsolv=2.647 density=0.00778 epsinf=1.75 I hope this help you. Yours, Jorge ------=_NextPart_000_0044_01CCAE1C.394B1140 Content-Type: text/x-vcard; name="Dr Jorge S Gancheff.vcf" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="Dr Jorge S Gancheff.vcf" BEGIN:VCARD VERSION:2.1 X-MS-SIGNATURE:YES N:Gancheff;Jorge;S.;Dr. FN:Dr. Jorge S. Gancheff ORG;CHARSET=3DWindows-1252:Facultad de Qu=EDmica, UdelaR TITLE;CHARSET=3DWindows-1252:Prof. Adjunto, Qu=EDmica Inorg=E1nica TEL;WORK;VOICE:(+598) 2924-9739 TEL;WORK;FAX:(+598) 2924-1906 ADR;WORK;PREF;CHARSET=3DWindows-1252:;;Av. Gral. Flores = 2124;11800-Montevideo;Uruguay;;Estados Unidos de Am=E9rica LABEL;WORK;PREF;ENCODING=3DQUOTED-PRINTABLE:Av. Gral. Flores = 2124=3D0D=3D0A=3D 11800-Montevideo, Uruguay ADR;HOME;CHARSET=3DWindows-1252:;;H=FCfferstrasse = 61;M=FCnster;;48149;Germany LABEL;HOME;CHARSET=3DWindows-1252;ENCODING=3DQUOTED-PRINTABLE:H=3DFCffers= trasse 61=3D0D=3D0A=3D =3D0D=3D0A=3D 48149, M=3DFCnster=3D0D=3D0A=3D Germany X-MS-OL-DEFAULT-POSTAL-ADDRESS:2 EMAIL;PREF;INTERNET:jorge : fq.edu.uy X-MS-OL-DESIGN;CHARSET=3Dutf-8: REV:20100831T155015Z END:VCARD ------=_NextPart_000_0044_01CCAE1C.394B1140-- From owner-chemistry@ccl.net Mon Nov 28 21:50:03 2011 From: "Mark Zottola mzottola~~gmail.com" To: CCL Subject: CCL:G: How To Specify DMF Solvent In Gaussian Input Message-Id: <-45944-111128174508-2128-3+lmdPsRxMn3gmRN1H1Zeg * server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=bcaec520f47391d7cf04b2d340d7 Date: Mon, 28 Nov 2011 17:44:57 -0500 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola---gmail.com] --bcaec520f47391d7cf04b2d340d7 Content-Type: text/plain; charset=ISO-8859-1 At the risk of being puckish, rtfm. DMF is listed in the Gaussian manual. The following link contains the information you need: http://www.gaussian.com/g_tech/g_ur/k_scrf.htm Mark On Mon, Nov 28, 2011 at 4:11 PM, P.D.Jarowski-#-surrey.ac.uk < owner-chemistry,ccl.net> wrote: > Hi, > > This answer may be annoying, but you could try acetonitrile > (SCRF=(PCM,CH3CN)). I have found that it is a good substitute for DMF. > Else, you will need to collect the solvent parameters for DMF from another > program or from the literature. > > Best of Luck > > Peter > > On 11/28/11 6:49 PM, "Vel Murugan G murugan4chemistry^^gmail.com" > wrote: > > > > Sent to CCL by: "Vel Murugan G" [murugan4chemistry,+,gmail.com] > Dear CClers > I need to run a PCM calculation with dimethylformamide DMF) as the > solvent. I was trying to specify DMF using the PCM model in Gaussian which > is not mentioned in the calculation part of the Gauss View. Does anyone > know how to specify DMF solvent in Gaussian input? Kindly help me. > > Thanks in advance > > With Regards > VELMURUGAN G > > > --bcaec520f47391d7cf04b2d340d7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
At the risk of being puckish, rtfm.
=A0
DMF is lis= ted in the Gaussian manual.=A0 The following link contains the information = you need:
=A0
=A0
Mark
On Mon, Nov 28,= 2011 at 4:11 PM, P.D.Jarowski-#-surrey.ac.= uk <own= er-chemistry,ccl.net> wrote:
Hi,

This answer may be annoying, but you could try acetonitrile (SCRF=3D(PCM,CH= 3CN)). I have found that it is a good substitute for DMF. Else, you will ne= ed to collect the solvent parameters for DMF from another program or from t= he literature.

Best of Luck

Peter

On 11/28/11 6:49 PM, "Vel Murugan G murugan4chemistry^^gmail.com" <owner-chemistry_._<= a href=3D"http://ccl.net" target=3D"_blank">ccl.net> wrote:



Sent to CCL by: "Vel Murugan G" [murugan4chemistry,+,gmail.com]
Dear CClers
=A0 =A0 =A0 =A0I need to run a PCM calculation with dimethylformamide DMF)= as the solvent. I was trying to specify DMF using the PCM model in Gaussia= n which is not mentioned in the calculation part of the Gauss View. Does an= yone know how to specify DMF solvent in Gaussian input? Kindly help me.

Thanks in advance

With Regards
VELMURUGAN G



--bcaec520f47391d7cf04b2d340d7--