From owner-chemistry@ccl.net Tue Mar 24 00:09:00 2015 From: "conor douglas parks coparks2012=gmail.com" To: CCL Subject: CCL: Solvating box with tinker issue/question Message-Id: <-51181-150323221608-15424-mbsDk/pSSeJCx7PyT6urxA.@.server.ccl.net> X-Original-From: "conor douglas parks" Date: Mon, 23 Mar 2015 22:16:07 -0400 Sent to CCL by: "conor douglas parks" [coparks2012(a)gmail.com] Hello everyone, I am having issues trying to solvate an orthogonal box with 3000 tetrolic acid molecules and 3000 CCl4 molecules in a box with axes of length 11 nm. This corresponds to a liquid density of 0.98 g/cm^3. The xyz file I am using, which contains the OPLS atom types I have assigned, for tetrolic acid is given as follows: 10 1 CT 4.395 -0.989 1.684 80 2 8 9 10 2 CZ 5.255 0.114 1.281 769 3 1 3 CZ 5.957 1.000 0.949 769 2 4 4 C 6.879 2.024 0.528 209 5 6 3 5 O 7.993 1.803 0.127 210 4 6 OH 6.377 3.232 0.607 211 4 7 7 HO 6.978 3.845 0.360 212 6 8 HC 3.672 -0.555 2.476 85 1 9 HC 4.190 -1.559 1.042 85 1 10 HC 4.752 -1.595 2.391 85 1 Similarly for CCL4 5 1 CT 0.000000 0.000000 0.000000 48 2 3 4 5 2 Cl 0.000000 0.000000 1.750000 49 1 3 Cl 1.650000 0.000000 -0.590000 49 1 4 Cl -0.830000 -1.430000 -0.590000 49 1 5 Cl -0.830000 1.430000 -0.590000 49 1 I had to assign the following additional torsional parameters to TTA, which is included in my tink.key file given here parameters oplsaa.prm angle 5 3 19 70.00 108.00 angle 4 3 19 80.00 120.40 angle 3 19 19 150.00 180.00 torsion 4 3 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 torsion 5 3 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 torsion 19 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 neighbor-list a-axis 110.00 vdw-cutoff 12.00 ewald ewald-cutoff 12.00 I solvated the box by first creating a solvated CCL4 box, a solvated TTA box, and then adding the two. Specifically, ./xyzedit.x ccl4.xyz -k tink.key 17 3000 110.00 ./xyzedit.x tta.xyz -k tink.key 17 3000 110.00 ./xyzedit.x tta.xyz_4 -k tink.key 18 chlor.xyz_2 ./minimize.x tta.xyz_3 -k tink.key 1.0 When I do this, only 1408 CCl4 molecules make it into the solvated tta/ccl4 system at a system density of 0.69 g/cm^3. The energy minimization then ends with a termination due to small fct, the energy is some monstrous small number and the gradient is still large O(10^8). When I look at the resulting file in VMD, many TTA molecules, which should be linear, are bent into strange geometries. I don't know if this is an issue with the force field I have chosen, or if I am doing something else wrong, which I would guess is much more likely. Would someone comment on whether I am doing the correct procedure for solvating a box in tinker with two different molecules, and why my energy minimization seems to be giving me strange geometries? Also I need to make a system corresponding to the correct density, so any comments on how I can make sure I get the right number of solvent molecules in the box would be greatly appreciated. Thanks From owner-chemistry@ccl.net Tue Mar 24 02:23:00 2015 From: "berger%chem.helsinki.fi" To: CCL Subject: CCL:G: Gaussian IR frequency calculation Message-Id: <-51182-150324021856-27972-L3MT4BASE3yHumMMyj18rQ ~ server.ccl.net> X-Original-From: berger++chem.helsinki.fi Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 24 Mar 2015 08:18:24 +0200 MIME-Version: 1.0 Sent to CCL by: berger[a]chem.helsinki.fi Hello, 300-400 cm-1 in the whole range also in my eyes seems much too large. Are you calculating the correct molecule? Is the experimental data correct? Are there impurities in the compound / solvens, ...? Is there a overall similarity between computed and experimental spectrum? Cheers B > Sent to CCL by: Robert Molt [r.molt.chemical.physics]![gmail.com] > I respectfully disagree with the claim that KS-DFT functionals get 97% > accuracy of the correct value, and the remaining 3% is mostly > anharmonic. That assumes that KS-DFT functionals are describing electron > correlation perfectly, as opposed to it being an approximate method > varying in semi-empirical character from none to high. > > The mean absolute error over the G2 set of vibrational frequencies of > B3LYP is 31 wavenumbers (see the 1998 paper from Adamo and Barone), > obviously weighted more heavily for the higher values frequencies > statistically. The RMS error can be as high as 42 wavenumbers (1993 > Pople paper). > > The first harmonic mode of many molecules is often small, and the > percent error is much higher on this first mode (independent of harmonic > vs. anharmonic). > > On 3/23/15 8:51 PM, Abrash, Samuel sabrash%a%richmond.edu wrote: >> Sent to CCL by: "Abrash, Samuel" [sabrash|a|richmond.edu] >> With an appropriate functional with a good basis set, dft should get you >> to within about 97% of the correct value. The remainder of the error >> will be due to the harmonic approximation. Adding an anharmonic >> correction can get you to within 99%. >> >> Sent from my iPhone >> >>> On Mar 23, 2015, at 8:45 PM, zborowsk zborowsk^chemia.uj.edu.pl >>> wrote: >>> >>> >>> Sent to CCL by: zborowsk [zborowsk^chemia.uj.edu.pl] >>> W dniu 2015-03-23 19:26, ggotelli()kaliumtech.com napisał(a): >>>> Sent to CCL by: [ggotelli[]kaliumtech.com] >>>> Thank you all for your help! >>>> I'll condense all my notes in the same mail. >>>> >>>> Krzysztof , yes I observed the difference in the whole spectrum. >>> Well, something strange. 300-400 cm-1 difference between theory and >>> experiment around 3000 cm-1 and also around 100 cm-1?? By the way, do >>> you have positive or negative (imaginary) frequencies around 100??? >>> >>> >>>> Serdar, the molecule that I 'm trying to calculate and where I have >>>> the >>>> differences is a dimer derived from dilactide. To estimate a scaling >>>> factor >>>> my reference molecule is dilactide in itself, which in turn has little >>>> differences between the calculated spectrum and the real one, >>>> depending on >>>> the peaks. >>>> >>>> André, thanks for the scaling factor reference. >>>> >>>> Stent, the polymer spectrum was made with an ATR device and without >>>> solvent. >>>> Because of this all calculations have done in vacuum. >>>> >>>> Robert, thanks for all your comments, they made me realize that my >>>> error was >>>> trying to adjust a dimer spectrum to a polymer spectrum, what are, of >>>> course, very different things. Although the dimer peaks are displaced >>>> with >>>> respect to those of the polymer, it can be seen from the GView >>>> animation >>>> that they correspond to what is expected, beyond the displacement >>>> involved. >>>> >>>> Regards! >>>> Gustavo Gotelli >>>> Polymer Synthesis >>>> Pharmaceutical Technology Department >>>> Faculty of Pharmacy and Biochemistry >>>> Buenos Aires University >>>> Argentina >>>> >>>> -----Mensaje original----- >>>> De: owner-chemistry+ggotelli==kaliumtech.com a ccl.net >>>> [mailto:owner-chemistry+ggotelli==kaliumtech.com a ccl.net] En nombre >>>> de >>>> Víctor Luaña Cabal victor^^fluor.quimica.uniovi.es >>>> Enviado el: sábado, 21 de marzo de 2015 21:16 >>>> Para: Gotelli, Gustavo A >>>> Asunto: CCL: Gaussian IR frequency calculation >>>> >>>> >>>> Sent to CCL by: Vctor Luaa Cabal >>>> [victor]|[fluor.quimica.uniovi.es] >>>> On Sat, Mar 21, 2015 at 05:56:44PM -0400, Robert Molt >>>> r.molt.chemical.physics],[gmail.com wrote: >>>>> Sent to CCL by: Robert Molt [r.molt.chemical.physics---gmail.com] >>>>> Moreover, you are using the B3LYP functional. It has limited >>>>> accuracy, >>>>> depending on the system specifics. If it is a multi-reference >>>>> problem, >>>>> great care is necessary. >>>>> >>>>> Also note that you can only compare the TOTAL spectrum, not any one >>>>> peak. >>>> Robert, >>>> >>>> 1) Let me take your highly correct advise to remember to the newest >>>> generations that the role on computational chemistry is not being >>>> able to reproduce the number of the experiment. >>>> >>>> 2) The experiment helps in modulating our calculations, and the final >>>> objective is a perfect reprodution of the experiment. >>>> >>>> 3) But the reason is not substituting experiments. The reason is that >>>> in the processs of mimicking it we learn the rules that govern >>>> Nature. >>>> >>>> 4) There are too many questions in this forum that tend to ignore >>>> this rule and it is important to remember it again and again. >>>> >>>> Best regards, >>>> Dr. Víctor Luaña >>>> -- >>>> . . "The hardest part in solving a problem is recognizing >>>> / `' \ its existence. Learning the causes CAN be the road to >>>> /(o)(o)\ the solution." >>>> /`. \/ .'\ -- ¿? >>>> / '`'` \ "Lo mediocre es peor que lo bueno, pero también es peor >>>> | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una >>>> | >>>> |'`'`| | actitud" >>>> \/`'`'`'\/ -- Jorge Wasenberg, 2015 >>>> ===(((==)))==================================+========================= >>>> ! Dr.Víctor Luaña ! Mediocre is worse >>>> than >>>> ! Departamento de Química Física y Analítica ! good, but it is also >>>> ! >>>> Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because >>>> ! e-mail: victor-#-fluor.quimica.uniovi.es ! mediocrity is not a >>>> grade, >>>> ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude >>>> +--------------------------------------------+ >>>> GroupPage : http://azufre.quimica.uniovi.es/ (being >>>> reworked)http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- >>> https://www.youtube.com/watch?v=IGyfx3Pmeyk >>> Krzysztof K. Zborowski >>> Faculty of Chemistry >>> Jagiellonian University >>> 3 Ingardena Street >>> 30-060 Krakow >>> Poland >>> phone: +48(12)663-2067 >>> email: zborowsk(~)chemia.uj.edu.pl >>> gg 3817259 >>> skype kzys70 >>> www.chemia.uj.edu.pl/~zborowskhttp://www.ccl.net/chemistry/sub_unsub.shtml> >> > > -- > Dr. Robert Molt Jr. > r.molt.chemical.physics=-=gmail.com > Nigel Richards Research Group > Department of Chemistry & Chemical Biology > Indiana University-Purdue University Indianapolis > LD 326 > 402 N. Blackford St. > Indianapolis, IN 46202> > > From owner-chemistry@ccl.net Tue Mar 24 05:46:01 2015 From: "Ahmad Ziaee ahmad.ziaee*ul.ie" To: CCL Subject: CCL:G: Error Message-Id: <-51183-150324054453-1835-ilHWKDfyBKXNUDg+wVYJ8A]=[server.ccl.net> X-Original-From: "Ahmad Ziaee" Date: Tue, 24 Mar 2015 05:44:52 -0400 Sent to CCL by: "Ahmad Ziaee" [ahmad.ziaee%%ul.ie] Hi All, I want to do a PBC optimization with the input below: --------------------- %nprocshared=24 %mem=50GB # opt=calcfc pbepbe/gen pseudo=read scf=maxcycle=512 PBC optimization 0 1 Zn 3.57045000 3.57045000 3.80340000 F 3.57045000 3.57045000 1.74652128 F 2.39862831 2.39862831 0.00000000 N 3.57045000 1.39818822 3.80340000 C 3.57045000 0.70409274 2.70421740 H 3.57045000 1.15254126 1.89028980 Si 3.57045000 3.57045000 0.00000000 F 3.57045000 3.57045000 5.86027872 F 4.74227169 2.39862831 0.00000000 F 4.74227169 4.74227169 0.00000000 F 2.39862831 4.74227169 0.00000000 N 5.74271178 3.57045000 3.80340000 N 3.57045000 5.74271178 3.80340000 N 1.39818822 3.57045000 3.80340000 C 6.43680726 3.57045000 2.70421740 C 3.57045000 6.43680726 2.70421740 C 0.70409274 3.57045000 2.70421740 C 3.57045000 6.43680726 4.90258260 C 0.70409274 3.57045000 4.90258260 C 3.57045000 0.70409274 4.90258260 C 6.43680726 3.57045000 4.90258260 H 5.98835874 3.57045000 1.89028980 H 3.57045000 5.98835874 1.89028980 H 1.15254126 3.57045000 1.89028980 H 3.57045000 5.98835874 5.71651020 H 1.15254126 3.57045000 5.71651020 H 3.57045000 1.15254126 5.71651020 H 5.98835874 3.57045000 5.71651020 Tv 7.14090000 0.00000000 0.00000000 Tv 0.00000000 7.14090000 0.00000000 Tv 0.00000000 0.00000000 7.60680000 C F H Si N 0 6-31G(d,p) **** Zn 0 LANL2DZ **** Zn 0 LANL2DZ ----------------------- After one step and having the SCF done and getting the energy I get a strange error like below: ECPInt: NShTT= 5778 NPrTT= 35633 LenC2= 5258 LenP2D= 18786. LDataN: DoStor=T MaxTD1= 6 Len= 172 Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 29 centers at a time, making 1 passes. Calling FoFCou, ICntrl= 3507 FMM=T I1Cent= 0 AccDes= 0.00D+00. NB too large for integers on this machine. Error termination via Lnk1e in /ichec/packages/gaussian/09d01/l1110.exe at Mon Mar 23 22:26:39 2015. Job cpu time: 0 days 5 hours 10 minutes 42.3 seconds. File lengths (MBytes): RWF= 37381 Int= 0 D2E= 0 Chk= 696 Scr= 1 ------------------------- Would you please let me know what can I do in order to solve this error? I even increased the shared memory amount but it didnt work. Thanks a million, Ahmad From owner-chemistry@ccl.net Tue Mar 24 06:20:01 2015 From: "=?UTF-8?Q?Serdar_Bado=C4=9Flu?= serdarbadoglu * gmail.com" To: CCL Subject: CCL:G: Gaussian IR frequency calculation Message-Id: <-51184-150324061258-11081-8es0XnHrSoX8juc+EmKsdA_._server.ccl.net> X-Original-From: =?UTF-8?Q?Serdar_Bado=C4=9Flu?= Content-Type: multipart/alternative; boundary=089e0158b938681ac90512060624 Date: Tue, 24 Mar 2015 12:12:50 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Serdar_Bado=C4=9Flu?= [serdarbadoglu%gmail.com] --089e0158b938681ac90512060624 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Gustavo, 300-400 cm-1 deviation between the theory and experiment on the whole spectrum made me think that you're calculating a wrong structure. You can use a dimer spectrum to make assignments for a polymer spectrum ( see our article Spectrochim. Acta A 134 (2015) 267-275 ). As I could understand you're dealing with a polymer built up from a monomer which has several isomers in real. Hence, first you should determine the tacticity of your chain. Then you should correctly determine what the repeating unit is. And do your calculations on it. Pick up the scaling factor from literature. But be aware that even for a certain level theory there may be more than one scaling factors reported, and sometimes a less known factor can produce better results than a well known factor. Regards On Tue, Mar 24, 2015 at 8:18 AM, berger%chem.helsinki.fi < owner-chemistry/a\ccl.net> wrote: > > Sent to CCL by: berger[a]chem.helsinki.fi > Hello, > > 300-400 cm-1 in the whole range also in my eyes seems much too large. Are > you calculating the correct molecule? Is the experimental data correct? > Are there impurities in the compound / solvens, ...? Is there a overall > similarity between computed and experimental spectrum? > > Cheers > B > > > Sent to CCL by: Robert Molt [r.molt.chemical.physics]![gmail.com] > > I respectfully disagree with the claim that KS-DFT functionals get 97% > > accuracy of the correct value, and the remaining 3% is mostly > > anharmonic. That assumes that KS-DFT functionals are describing electro= n > > correlation perfectly, as opposed to it being an approximate method > > varying in semi-empirical character from none to high. > > > > The mean absolute error over the G2 set of vibrational frequencies of > > B3LYP is 31 wavenumbers (see the 1998 paper from Adamo and Barone), > > obviously weighted more heavily for the higher values frequencies > > statistically. The RMS error can be as high as 42 wavenumbers (1993 > > Pople paper). > > > > The first harmonic mode of many molecules is often small, and the > > percent error is much higher on this first mode (independent of harmoni= c > > vs. anharmonic). > > > > On 3/23/15 8:51 PM, Abrash, Samuel sabrash%a%richmond.edu wrote: > >> Sent to CCL by: "Abrash, Samuel" [sabrash|a|richmond.edu] > >> With an appropriate functional with a good basis set, dft should get y= ou > >> to within about 97% of the correct value. The remainder of the error > >> will be due to the harmonic approximation. Adding an anharmonic > >> correction can get you to within 99%. > >> > >> Sent from my iPhone > >> > >>> On Mar 23, 2015, at 8:45 PM, zborowsk zborowsk^chemia.uj.edu.pl > >>> wrote: > >>> > >>> > >>> Sent to CCL by: zborowsk [zborowsk^chemia.uj.edu.pl] > >>> W dniu 2015-03-23 19:26, ggotelli()kaliumtech.com napisa=C3=85=E2=80= =9A(a): > >>>> Sent to CCL by: [ggotelli[]kaliumtech.com] > >>>> Thank you all for your help! > >>>> I'll condense all my notes in the same mail. > >>>> > >>>> Krzysztof , yes I observed the difference in the whole spectrum. > >>> Well, something strange. 300-400 cm-1 difference between theory and > >>> experiment around 3000 cm-1 and also around 100 cm-1?? By the way, d= o > >>> you have positive or negative (imaginary) frequencies around 100??? > >>> > >>> > >>>> Serdar, the molecule that I 'm trying to calculate and where I have > >>>> the > >>>> differences is a dimer derived from dilactide. To estimate a scaling > >>>> factor > >>>> my reference molecule is dilactide in itself, which in turn has litt= le > >>>> differences between the calculated spectrum and the real one, > >>>> depending on > >>>> the peaks. > >>>> > >>>> Andr=C3=83=C2=A9, thanks for the scaling factor reference. > >>>> > >>>> Stent, the polymer spectrum was made with an ATR device and without > >>>> solvent. > >>>> Because of this all calculations have done in vacuum. > >>>> > >>>> Robert, thanks for all your comments, they made me realize that my > >>>> error was > >>>> trying to adjust a dimer spectrum to a polymer spectrum, what are, o= f > >>>> course, very different things. Although the dimer peaks are displace= d > >>>> with > >>>> respect to those of the polymer, it can be seen from the GView > >>>> animation > >>>> that they correspond to what is expected, beyond the displacement > >>>> involved. > >>>> > >>>> Regards! > >>>> Gustavo Gotelli > >>>> Polymer Synthesis > >>>> Pharmaceutical Technology Department > >>>> Faculty of Pharmacy and Biochemistry > >>>> Buenos Aires University > >>>> Argentina > >>>> > >>>> -----Mensaje original----- > >>>> De: owner-chemistry+ggotelli=3D=3Dkaliumtech.com a ccl.net > >>>> [mailto:owner-chemistry+ggotelli=3D=3Dkaliumtech.com a ccl.net] En n= ombre > >>>> de > >>>> V=C3=83=C2=ADctor Lua=C3=83=C2=B1a Cabal victor^^fluor.quimica.uniov= i.es > >>>> Enviado el: s=C3=83=C2=A1bado, 21 de marzo de 2015 21:16 > >>>> Para: Gotelli, Gustavo A > >>>> Asunto: CCL: Gaussian IR frequency calculation > >>>> > >>>> > >>>> Sent to CCL by: V=C3=ADctor Lua=C3=B1a Cabal > >>>> [victor]|[fluor.quimica.uniovi.es] > >>>> On Sat, Mar 21, 2015 at 05:56:44PM -0400, Robert Molt > >>>> r.molt.chemical.physics],[gmail.com wrote: > >>>>> Sent to CCL by: Robert Molt [r.molt.chemical.physics---gmail.com] > >>>>> Moreover, you are using the B3LYP functional. It has limited > >>>>> accuracy, > >>>>> depending on the system specifics. If it is a multi-reference > >>>>> problem, > >>>>> great care is necessary. > >>>>> > >>>>> Also note that you can only compare the TOTAL spectrum, not any one > >>>>> peak. > >>>> Robert, > >>>> > >>>> 1) Let me take your highly correct advise to remember to the newest > >>>> generations that the role on computational chemistry is not being > >>>> able to reproduce the number of the experiment. > >>>> > >>>> 2) The experiment helps in modulating our calculations, and the fina= l > >>>> objective is a perfect reprodution of the experiment. > >>>> > >>>> 3) But the reason is not substituting experiments. The reason is tha= t > >>>> in the processs of mimicking it we learn the rules that govern > >>>> Nature. > >>>> > >>>> 4) There are too many questions in this forum that tend to ignore > >>>> this rule and it is important to remember it again and again. > >>>> > >>>> Best regards, > >>>> Dr. V=C3=83=C2=ADctor Lua=C3=83=C2=B1a > >>>> -- > >>>> . . "The hardest part in solving a problem is recognizing > >>>> / `' \ its existence. Learning the causes CAN be the road to > >>>> /(o)(o)\ the solution." > >>>> /`. \/ .'\ -- =C3=82=C2=BF? > >>>> / '`'` \ "Lo mediocre es peor que lo bueno, pero tambi=C3=83=C2= =A9n es peor > >>>> | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es u= na > >>>> | > >>>> |'`'`| | actitud" > >>>> \/`'`'`'\/ -- Jorge Wasenberg, 2015 > >>>> > =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > >>>> ! Dr.V=C3=83=C2=ADctor Lua=C3=83=C2=B1a != Mediocre is worse > >>>> than > >>>> ! Departamento de Qu=C3=83=C2=ADmica F=C3=83=C2=ADsica y Anal=C3=83= =C2=ADtica ! good, but it is also > >>>> ! > >>>> Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because > >>>> ! e-mail: victor-#-fluor.quimica.uniovi.es ! mediocrity is not a > >>>> grade, > >>>> ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude > >>>> +--------------------------------------------+ > >>>> GroupPage : http://azufre.quimica.uniovi.es/ (being > >>>> reworked)http://www.ccl.net/chemist= ry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- > >>> https://www.youtube.com/watch?v=3DIGyfx3Pmeyk > >>> Krzysztof K. Zborowski > >>> Faculty of Chemistry > >>> Jagiellonian University > >>> 3 Ingardena Street > >>> 30-060 Krakow > >>> Poland > >>> phone: +48(12)663-2067 > >>> email: zborowsk(~)chemia.uj.edu.pl > >>> gg 3817259 > >>> skype kzys70 > >>> > www.chemia.uj.edu.pl/~zborowskhttp://www.ccl.net/chemistry/sub_unsub.shtm= l > > > >> > > > > -- > > Dr. Robert Molt Jr. > > r.molt.chemical.physics=3D-=3Dgmail.com > > Nigel Richards Research Group > > Department of Chemistry & Chemical Biology > > Indiana University-Purdue University Indianapolis > > LD 326 > > 402 N. Blackford St. > > Indianapolis, IN 46202> > > > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Serdar BADO=C4=9ELU, Ph.D. Gazi =C3=9Cniversitesi Fizik B=C3=B6l=C3=BCm=C3=BC --089e0158b938681ac90512060624 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Gustavo,

300-400 cm-1 deviation be= tween the theory and experiment on the whole spectrum made me think that yo= u're calculating a wrong structure. You can use=C2=A0a dimer spectrum to make assignments for a polym= er spectrum ( see our article Spectrochim. Acta A 134 (2015) 267-275 ). As = I could understand you're dealing with a polymer built up from a monome= r which has several isomers in real. Hence, first you should determine the = tacticity of your chain.=C2=A0Then you should = correctly determine what the repeating unit is. And do your calculations on= it. Pick up the scaling factor from literature. But be aware that even for= a certain level theory there may be more than one scaling factors reported= , and sometimes a less known factor can produce better results than a well = known factor.

Regards=

On Tue, Mar 24, 2015 at 8:18 AM, berger%chem.helsinki.fi <owner-chemistry/a\ccl.net> wrot= e:

Sent to CCL by: berger[a]chem.helsinki.fi
Hello,

300-400 cm-1 in the whole range also in my eyes seems much too large. Are you calculating the correct molecule? Is the experimental data correct?
Are there impurities in the compound / solvens, ...? Is there a overall
similarity between computed and experimental spectrum?

Cheers
=C2=A0 B

> Sent to CCL by: Robert Molt [r.molt.chemical.physics]![gmail.com]
> I respectfully disagree with the claim that KS-DFT functionals get 97%=
> accuracy of the correct value, and the remaining 3% is mostly
> anharmonic. That assumes that KS-DFT functionals are describing electr= on
> correlation perfectly, as opposed to it being an approximate method > varying in semi-empirical character from none to high.
>
> The mean absolute error over the G2 set of vibrational frequencies of<= br> > B3LYP is 31 wavenumbers (see the 1998 paper from Adamo and Barone), > obviously weighted more heavily for the higher values frequencies
> statistically. The RMS error can be as high as 42 wavenumbers (1993 > Pople paper).
>
> The first harmonic mode of many molecules is often small, and the
> percent error is much higher on this first mode (independent of harmon= ic
> vs. anharmonic).
>
> On 3/23/15 8:51 PM, Abrash, Samuel sabrash%a%richmond.edu wrote:
>> Sent to CCL by: "Abrash, Samuel" [sabrash|a|richmond.edu]
>> With an appropriate functional with a good basis set, dft should g= et you
>> to within about 97% of the correct value.=C2=A0 The remainder of t= he error
>> will be due to the harmonic approximation. Adding an anharmonic >> correction can get you to within 99%.
>>
>> Sent from my iPhone
>>
>>> On Mar 23, 2015, at 8:45 PM, zborowsk zborowsk^chemia.uj.edu.pl
>>> <owner-chemistry.:.ccl.net> wrote:
>>>
>>>
>>> Sent to CCL by: zborowsk [zborowsk^chemia.uj.edu.pl]
>>> W dniu 2015-03-23 19:26, ggotelli()kaliumtech.com napisa=C3=85=E2=80=9A(a)= :
>>>> Sent to CCL by: [ggotelli[]kaliumtech.com]
>>>> Thank you all for your help!
>>>> I'll condense all my notes in the same mail.
>>>>
>>>> Krzysztof , yes I observed the difference in the whole spe= ctrum.
>>> Well, something strange. 300-400 cm-1 difference between theor= y and
>>> experiment=C2=A0 around 3000 cm-1 and also around 100 cm-1?? B= y the way, do
>>> you have positive or negative (imaginary) frequencies around 1= 00???
>>>
>>>
>>>> Serdar, the molecule that I 'm trying to calculate and= where I have
>>>> the
>>>> differences is a dimer derived from dilactide. To estimate= a scaling
>>>> factor
>>>> my reference molecule is dilactide in itself, which in tur= n has little
>>>> differences between the calculated spectrum and the real o= ne,
>>>> depending on
>>>> the peaks.
>>>>
>>>> Andr=C3=83=C2=A9, thanks for the scaling factor ref= erence.
>>>>
>>>> Stent, the polymer spectrum was made with an ATR device an= d without
>>>> solvent.
>>>> Because of this all calculations have done in vacuum.
>>>>
>>>> Robert, thanks for all your comments, they made me realize= that my
>>>> error was
>>>> trying to adjust a dimer spectrum to a polymer spectrum, w= hat are, of
>>>> course, very different things. Although the dimer peaks ar= e displaced
>>>> with
>>>> respect to those of the polymer, it can be seen from the G= View
>>>> animation
>>>> that they correspond to what is expected, beyond the displ= acement
>>>> involved.
>>>>
>>>> Regards!
>>>> Gustavo Gotelli
>>>> Polymer Synthesis
>>>> Pharmaceutical Technology Department
>>>> Faculty of Pharmacy and Biochemistry
>>>> Buenos Aires University
>>>> Argentina
>>>>
>>>> -----Mensaje original-----
>>>> De: owner-chemistry+ggotelli=3D=3Dkaliumtech.com a ccl.net
>>>> [mailto:owne= r-chemistry+ggotelli=3D=3Dkaliumtech.com a cc= l.net] En nombre
>>>> de
>>>> V=C3=83=C2=ADctor Lua=C3=83=C2=B1a Cabal victor^^fluor.quimica.un= iovi.es
>>>> Enviado el: s=C3=83=C2=A1bado, 21 de marzo de 2015 21:16 >>>> Para: Gotelli, Gustavo A
>>>> Asunto: CCL: Gaussian IR frequency calculation
>>>>
>>>>
>>>> Sent to CCL by: V=C3=ADctor Lua=C3=B1a Cabal
>>>> [victor]|[fluor.quimica.uniovi.es]
>>>> On Sat, Mar 21, 2015 at 05:56:44PM -0400, Robert Molt
>>>> r.molt.chemical.physics],[gmail.com wrote:
>>>>> Sent to CCL by: Robert Molt [r.molt.chemical.physics---g= mail.com]
>>>>> Moreover, you are using the B3LYP functional. It has l= imited
>>>>> accuracy,
>>>>> depending on the system specifics. If it is a multi-re= ference
>>>>> problem,
>>>>> great care is necessary.
>>>>>
>>>>> Also note that you can only compare the TOTAL spectrum= , not any one
>>>>> peak.
>>>> Robert,
>>>>
>>>> 1) Let me take your highly correct advise to remember to t= he newest
>>>>=C2=A0 =C2=A0 generations that the role on computational ch= emistry is not being
>>>>=C2=A0 =C2=A0 able to reproduce the number of the experimen= t.
>>>>
>>>> 2) The experiment helps in modulating our calculations, an= d the final
>>>>=C2=A0 =C2=A0 objective is a perfect reprodution of the exp= eriment.
>>>>
>>>> 3) But the reason is not substituting experiments. The rea= son is that
>>>>=C2=A0 =C2=A0 in the processs of mimicking it we learn the = rules that govern
>>>>=C2=A0 =C2=A0 Nature.
>>>>
>>>> 4) There are too many questions in this forum that tend to= ignore
>>>>=C2=A0 =C2=A0 this rule and it is important to remember it = again and again.
>>>>
>>>> Best regards,
>>>>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Dr. = V=C3=83=C2=ADctor Lua=C3=83=C2=B1a
>>>> --
>>>>=C2=A0 =C2=A0 =C2=A0 .=C2=A0 .=C2=A0 =C2=A0 "The harde= st part in solving a problem is recognizing
>>>>=C2=A0 =C2=A0 =C2=A0/ `' \=C2=A0 =C2=A0its existence. L= earning the causes CAN be the road to
>>>>=C2=A0 =C2=A0 /(o)(o)\=C2=A0 the solution."
>>>>=C2=A0 =C2=A0/`. \/ .'\=C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 -- =C3=82=C2=BF?
>>>> /=C2=A0 =C2=A0'`'`=C2=A0 =C2=A0\ "Lo mediocre= es peor que lo bueno, pero tambi=C3=83=C2=A9n es peor
>>>> |=C2=A0 \'`'`/=C2=A0 | que lo mal= o, porque la mediocridad no es un grado, es una
>>>>=C2=A0 |
>>>> |'`'`|=C2=A0 | actitud"
>>>>=C2=A0 =C2=A0\/`'`'`'\/=C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 -- Jorge Wasenberg, 2015
>>>> =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>>>> !=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr.V=C3= =83=C2=ADctor Lua=C3=83=C2=B1a=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0! Mediocre is worse
>>>> than
>>>> ! Departamento de Qu=C3=83=C2=ADmica F=C3=83=C2=ADsica y A= nal=C3=83=C2=ADtica ! good, but it is also
>>>> !
>>>> Universidad de Oviedo, 33006-Oviedo, Spain ! worse than ba= d, because
>>>> ! e-mail:=C2=A0 =C2=A0victor-#-fluor.quimica.uniovi.es=C2=A0 =C2=A0!= mediocrity is not a
>>>> grade,
>>>> ! phone: +34-985-103491=C2=A0 fax: +34-985-103125 ! it is an attitude
>>>> +--------------------------------------------+
>>>> GroupPage : http://azufre.quimica.uniovi.es/=C2=A0 (being
>>>> reworked)http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= agehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.= txt--
>>> https://www.youtube.com/watch?v=3DIGyfx3Pmeyk
>>> Krzysztof K. Zborowski
>>> Faculty of Chemistry
>>> Jagiellonian University
>>> 3 Ingardena Street
>>> 30-060 Krakow
>>> Poland
>>> phone: +48(12)663-2067
>>> email: zborowsk(~)chemia.uj.edu.pl
>>> gg 3817259
>>> skype kzys70
>>> www.chemia.uj.edu.pl/~zbo= rowskhttp://www.ccl.net/chemistry/sub_unsub.shtml>
>>
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics=3D-=3Dgmail.com
> Nigel Richards Research Group
> Department of Chemistry & Chemical Biology
> Indiana University-Purdue University Indianapolis
> LD 326
> 402 N. Blackford St.
> Indianapolis, IN 46202>
>
>



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--
=
Serdar BADO=C4=9ELU, Ph.D.
Gazi =C3=9Cniv= ersitesi Fizik B=C3=B6l=C3=BCm=C3=BC
--089e0158b938681ac90512060624-- From owner-chemistry@ccl.net Tue Mar 24 09:48:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor ~~ fluor.quimica.uniovi.es" To: CCL Subject: CCL: Error Message-Id: <-51185-150324094428-9244-HXerKBiV3iM/d7r9fmxGPg a server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Tue, 24 Mar 2015 14:39:22 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor^fluor.quimica.uniovi.es] On Tue, Mar 24, 2015 at 05:44:52AM -0400, Ahmad Ziaee ahmad.ziaee*ul.ie wrote: > > Sent to CCL by: "Ahmad Ziaee" [ahmad.ziaee%%ul.ie] > Hi All, Ahmad, 1) Your system is VERY large. I advise you to start an approach in steps. First, try to optimize the geometry using a cheap and sure nethod like HF/3-21G. Then start a proccess of using the feometry from a level to start the calculation of un upper level of theory and basis sets. If the number of electrons in your system is even you can start at the HF = RHF level. If it is odd you could start from UHF. 2) That's basic quantum chemistry. If you need a good book on the subject you can try Quantum chemistry by I.N. Levine or Computational Organic Chemistry by S.M. Bachrach. Best regards, Dr. Vctor Luaa -- . . "The hardest part in solving a problem is recognizing / `' \ its existence. Learning the causes CAN be the road to /(o)(o)\ the solution." /`. \/ .'\ -- ? / '`'` \ "Lo mediocre es peor que lo bueno, pero tambin es peor | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una | |'`'`| | actitud" \/`'`'`'\/ -- Jorge Wasenberg, 2015 ===(((==)))==================================+========================= ! Dr.Vctor Luaa ! Mediocre is worse than ! Departamento de Qumica Fsica y Analtica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor]~[fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Tue Mar 24 13:22:01 2015 From: "Safiya Ess Amer amersaf85]~[yahoo.com" To: CCL Subject: CCL:G: Ghost atoms (symbol Bq) Message-Id: <-51186-150324130054-30999-e+yT/sVbQ3f5Rc8jc6k6eg!A!server.ccl.net> X-Original-From: "Safiya Ess Amer" Date: Tue, 24 Mar 2015 13:00:52 -0400 Sent to CCL by: "Safiya Ess Amer" [amersaf85||yahoo.com] Hello. Please, how can I use ghost atom with Cartesian coordinates? I have system of H2-Fe(OH)3 and use G03W for getting energy as function of more distances (Z) from center of H2 to Fe atom. I am calculating now each value of energy at some distance manually. I need to put ghost atom at center of H2, how can I do that to get PES. Can anyone help me in input file? I have geometry of the system. Thanks in advance Safiya Amer amersaf85-$-yahoo.com From owner-chemistry@ccl.net Tue Mar 24 13:56:00 2015 From: "Abrash, Samuel sabrash- -richmond.edu" To: CCL Subject: CCL:G: Gaussian IR frequency calculation Message-Id: <-51187-150324130319-31175-MqEBLsYsfZ9HhLhvA63Avw- -server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Tue, 24 Mar 2015 17:03:10 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash ~~ richmond.edu] So I think the data that Robert just cited supports my claim of a 3% error. In the range 4000 cm-1 to 400 cm-1, the mid-ir, a 3% error would range from 120 cm-1 to 12 cm-1 so a 31 cm-1 average seems to be a bit below 3%. The other support for my claim is to go to the CCCDB (I think that's the correct number of C's) hosted at NIST, and check out the correction factors. For the types of high quality functional/basis set combinations, the correction factors are greater than .97, again consistent with an error of ~3%. Samuel A. Abrash Associate Professor, Department of Chemistry Coordinator, Environmental Studies Program University of Richmond sabrash**richmond.edu Cell: (804) 363-2597 www.richmond.edu/~sabrash “At the time God created the world and desired to reveal the depth of His being from out of the hidden, the light came from darkness and they were joined together. Because of this, out of darkness came the light, and out of the hidden came the revealed and out of the good came evil and out of mercy came severe judgement, and everything is intertwined with everything else… the good inclination and the evil inclination, the right and the left.” The Zohar -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu**ccl.net [mailto:owner-chemistry+sabrash==richmond.edu**ccl.net] On Behalf Of Robert Molt r.molt.chemical.physics ~ gmail.com Sent: Monday, March 23, 2015 10:58 PM To: Abrash, Samuel Subject: CCL:G: Gaussian IR frequency calculation Sent to CCL by: Robert Molt [r.molt.chemical.physics]![gmail.com] I respectfully disagree with the claim that KS-DFT functionals get 97% accuracy of the correct value, and the remaining 3% is mostly anharmonic. That assumes that KS-DFT functionals are describing electron correlation perfectly, as opposed to it being an approximate method varying in semi-empirical character from none to high. The mean absolute error over the G2 set of vibrational frequencies of B3LYP is 31 wavenumbers (see the 1998 paper from Adamo and Barone), obviously weighted more heavily for the higher values frequencies statistically. The RMS error can be as high as 42 wavenumbers (1993 Pople paper). The first harmonic mode of many molecules is often small, and the percent error is much higher on this first mode (independent of harmonic vs. anharmonic). On 3/23/15 8:51 PM, Abrash, Samuel sabrash%a%richmond.edu wrote: > Sent to CCL by: "Abrash, Samuel" [sabrash|a|richmond.edu] With an > appropriate functional with a good basis set, dft should get you to within about 97% of the correct value. The remainder of the error will be due to the harmonic approximation. Adding an anharmonic correction can get you to within 99%. > > Sent from my iPhone > >> On Mar 23, 2015, at 8:45 PM, zborowsk zborowsk^chemia.uj.edu.pl wrote: >> >> >> Sent to CCL by: zborowsk [zborowsk^chemia.uj.edu.pl] W dniu >> 2015-03-23 19:26, ggotelli()kaliumtech.com napisał(a): >>> Sent to CCL by: [ggotelli[]kaliumtech.com] Thank you all for your >>> help! >>> I'll condense all my notes in the same mail. >>> >>> Krzysztof , yes I observed the difference in the whole spectrum. >> Well, something strange. 300-400 cm-1 difference between theory and experiment around 3000 cm-1 and also around 100 cm-1?? By the way, do you have positive or negative (imaginary) frequencies around 100??? >> >> >>> Serdar, the molecule that I 'm trying to calculate and where I have >>> the differences is a dimer derived from dilactide. To estimate a >>> scaling factor my reference molecule is dilactide in itself, which >>> in turn has little differences between the calculated spectrum and >>> the real one, depending on the peaks. >>> >>> André, thanks for the scaling factor reference. >>> >>> Stent, the polymer spectrum was made with an ATR device and without solvent. >>> Because of this all calculations have done in vacuum. >>> >>> Robert, thanks for all your comments, they made me realize that my >>> error was trying to adjust a dimer spectrum to a polymer spectrum, >>> what are, of course, very different things. Although the dimer peaks >>> are displaced with respect to those of the polymer, it can be seen >>> from the GView animation that they correspond to what is expected, beyond the displacement involved. >>> >>> Regards! >>> Gustavo Gotelli >>> Polymer Synthesis >>> Pharmaceutical Technology Department Faculty of Pharmacy and >>> Biochemistry Buenos Aires University Argentina >>> >>> -----Mensaje original----- >>> De: owner-chemistry+ggotelli==kaliumtech.com a ccl.net >>> [mailto:owner-chemistry+ggotelli==kaliumtech.com a ccl.net] En >>> nombre de Víctor Luaña Cabal victor^^fluor.quimica.uniovi.es Enviado >>> el: sábado, 21 de marzo de 2015 21:16 >>> Para: Gotelli, Gustavo A >>> Asunto: CCL: Gaussian IR frequency calculation >>> >>> >>> Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal >>> [victor]|[fluor.quimica.uniovi.es] >>> On Sat, Mar 21, 2015 at 05:56:44PM -0400, Robert Molt >>> r.molt.chemical.physics],[gmail.com wrote: >>>> Sent to CCL by: Robert Molt [r.molt.chemical.physics---gmail.com] >>>> Moreover, you are using the B3LYP functional. It has limited >>>> accuracy, depending on the system specifics. If it is a >>>> multi-reference problem, great care is necessary. >>>> >>>> Also note that you can only compare the TOTAL spectrum, not any one peak. >>> Robert, >>> >>> 1) Let me take your highly correct advise to remember to the newest >>> generations that the role on computational chemistry is not being >>> able to reproduce the number of the experiment. >>> >>> 2) The experiment helps in modulating our calculations, and the final >>> objective is a perfect reprodution of the experiment. >>> >>> 3) But the reason is not substituting experiments. The reason is that >>> in the processs of mimicking it we learn the rules that govern >>> Nature. >>> >>> 4) There are too many questions in this forum that tend to ignore >>> this rule and it is important to remember it again and again. >>> >>> Best regards, >>> Dr. Víctor Luaña >>> -- >>> . . "The hardest part in solving a problem is recognizing >>> / `' \ its existence. Learning the causes CAN be the road to >>> /(o)(o)\ the solution." >>> /`. \/ .'\ -- ¿? >>> / '`'` \ "Lo mediocre es peor que lo bueno, pero también es peor >>> | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es >>> |una | '`'`| | actitud" >>> \/`'`'`'\/ -- Jorge Wasenberg, 2015 >>> ===(((==)))==================================+========================= >>> ! Dr.Víctor Luaña ! Mediocre is worse than >>> ! Departamento de Química Física y Analítica ! good, but it is also ! >>> Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because >>> ! e-mail: victor-#-fluor.quimica.uniovi.es ! mediocrity is not a grade, >>> ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude >>> +--------------------------------------------+ >>> GroupPage : http://azufre.quimica.uniovi.es/ (being >>> reworked)http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.c >>> cl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- >> https://www.youtube.com/watch?v=IGyfx3Pmeyk >> Krzysztof K. Zborowski >> Faculty of Chemistry >> Jagiellonian University >> 3 Ingardena Street >> 30-060 Krakow >> Poland >> phone: +48(12)663-2067 >> email: zborowsk(~)chemia.uj.edu.pl >> gg 3817259 >> skype kzys70 >> www.chemia.uj.edu.pl/~zborowskhttp://www.ccl.net/chemistry/sub_unsub. >> shtml> > -- Dr. Robert Molt Jr. r.molt.chemical.physics=-=gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202http://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 Tue Mar 24 14:31:00 2015 From: "Susi Lehtola susi.lehtola~~alumni.helsinki.fi" To: CCL Subject: CCL: Error Message-Id: <-51188-150324130357-31219-jQdTvtEoNBwSdRJZC/Ylng]![server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 24 Mar 2015 10:03:43 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola[a]alumni.helsinki.fi] On 03/24/2015 06:39 AM, Vctor Luaa Cabal victor ~~ fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor^fluor.quimica.uniovi.es] > On Tue, Mar 24, 2015 at 05:44:52AM -0400, Ahmad Ziaee ahmad.ziaee*ul.ie wrote: >> >> Sent to CCL by: "Ahmad Ziaee" [ahmad.ziaee%%ul.ie] >> Hi All, > > Ahmad, > > 1) Your system is VERY large. I advise you to start an approach in steps. > First, try to optimize the geometry using a cheap and sure nethod > like HF/3-21G. Then start a proccess of using the feometry from a level > to start the calculation of un upper level of theory and basis sets. > If the number of electrons in your system is even you can start > at the HF = RHF level. If it is odd you could start from UHF. Since this is a PBC calculation, HF is *not* cheap: the long range exchange kills you. DFT will be much cheaper, and you might also want to consider using density fitting. If you need the accuracy of hybrid functionals, try using a short-range hybrid like HSE. My guess is that the problem are the force constants, since the system isn't that big and the basis set is very small. If you drop the calcfc argument, it should run. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola^-^alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Mar 24 15:24:00 2015 From: "Guenter Grethe ggrethe|att.net" To: CCL Subject: CCL: CINF-RSC Scholarships - Last Call Message-Id: <-51189-150324150539-29223-kAEBiMLp7edpIBtzYlPIgw=server.ccl.net> X-Original-From: "Guenter Grethe" Date: Tue, 24 Mar 2015 15:05:37 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe ~ att.net] The deadline for submitting abstracts to apply for the 2015 CINF-RSC scholarships to be awarded at the ACS meeting in Boston is approaching fast (March 2015) 2015 CINF Scholarship for Scientific Excellence Sponsored by the Royal Society of Chemistry The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by the Royal Society of Chemistry (RSC) is designed to reward students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to three scholarships valued at $1,000 each will be presented at the 250th ACS National Meeting in Boston, MA, August 16 August 20, 2015. Student applicants must be enrolled at a certified college or university; postdoctoral fellows are also invited to apply. They will present a poster during the Welcoming Reception of the Division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through MAPS, the abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe,+,att.net, that you are applying for a scholarship. Submit your abstract to http://maps.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract in the CINF program for the session CINF Scholarships for Scientific Excellence: Student Poster Competition. MAPS is now open for abstract submission and will close on March 29, 2015. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by June 20, 2015. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Guenter Grethe From owner-chemistry@ccl.net Tue Mar 24 19:01:01 2015 From: "Eduardo edulsa()ufpr.br" To: CCL Subject: CCL:G: Ghost atoms (symbol Bq) Message-Id: <-51190-150324185922-19559-oGuO15V1E9bplrR8YGqk2Q#server.ccl.net> X-Original-From: Eduardo Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 24 Mar 2015 19:59:07 -0300 MIME-Version: 1.0 Sent to CCL by: Eduardo [edulsa/a\ufpr.br] Dear Safiya > Sent to CCL by: "Safiya Ess Amer" [amersaf85||yahoo.com] > Hello. > Please, how can I use ghost atom with Cartesian coordinates? > I have system of H2-Fe(OH)3 and use G03W for getting energy as function of > more distances (Z) from center of H2 to Fe atom. I am calculating now each > value of energy at some distance manually. I need to put ghost atom at center > of H2, how can I do that to get PES. > > Can anyone help me in input file? > I have geometry of the system. > > Thanks in advance > > Safiya Amer > amersaf85]^[yahoo.com > > I used ghost atoms a long time ago, but if I can remember, the symbol for it is "X" instead "Bq". Cheers Eduardo> > From owner-chemistry@ccl.net Tue Mar 24 19:35:00 2015 From: "Lela Vukovic Lvukov1---illinois.edu" To: CCL Subject: CCL: Hands On Computational Biophysics Workshop (Lake Tahoe, Aug 3-7 2015) Message-Id: <-51191-150324165856-28191-F/SoSQF/3yivQlzTQSGa0Q]-[server.ccl.net> X-Original-From: "Lela Vukovic" Date: Tue, 24 Mar 2015 16:58:54 -0400 Sent to CCL by: "Lela Vukovic" [Lvukov1]^[illinois.edu] The Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the University of Illinois at Urbana-Champaign (www.uiuc.edu), announces a "Hands-On" Workshop on Computational Biophysics http://www.ks.uiuc.edu/Training/Workshop/LakeTahoe2015/ to be held August 3-7, 2015 at the Granlibakken Conference Center in Tahoe City, California. Application, selection, and notification of participants is on-going through July 15, 2015. The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and parameterizing new molecules, simulating membrane proteins and ion channels, modeling nucleic acid systems, computational nano-bio, and evolutionary algorithms and network dynamics. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. Enrollment limited to 24 participants. The workshop will be held August 3-7, 2015. All participants are required to bring their own laptop, prepared for use in workshop tutorial sessions. Course materials will be provided. The workshop is sponsored by the National Institute of General Medical Sciences (www.nigms.nih.gov), and the NIH Center for Macromolecular Modeling and Bioinformatics. We look forward to receiving your application! TCBG Workshop Organizers Email: workshop+laketahoe2015^-^ks.uiuc.edu From owner-chemistry@ccl.net Tue Mar 24 20:10:01 2015 From: "Layfield, Joshua P. jlayfield**stthomas.edu" To: CCL Subject: CCL:G: Ghost atoms (symbol Bq) Message-Id: <-51192-150324182156-3760-hfN7HZ/8nwubscc8pMREtA]-[server.ccl.net> X-Original-From: "Layfield, Joshua P." Content-ID: Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 24 Mar 2015 22:21:25 +0000 MIME-Version: 1.0 Sent to CCL by: "Layfield, Joshua P." [jlayfield _ stthomas.edu] Safiya, If you want to do a partially optimized scan something like this should work. (Please note that my method and geometry are not great). By defining the two hydrogen positions relative to the the dummy atom (xx) you can scan the h2 molecule as a unit. Also, if you want to do a frozen scan you also freeze the additional degrees of freedom at a good geometry by adding the F flag. Hope this helps! #HF/6-31G POPT(z-matrix) Scanning the intermolecular distance between Fe(OH)3 and H2 1 1 fe o 1 ofe2 o 1 ofe3 2 ofeo3 o 1 ofe4 2 ofeo4 3 dih4 xx 1 xxfe5 2 xxfeo5 3 dih5 h 2 ho6 1 hofe6 3 dih6 h 3 ho7 1 hofe7 2 dih7 h 4 ho8 1 hofe8 2 dih8 h 5 hxx9 1 hxxfe9 2 dih9 h 5 hxx10 1 hxxfe10 9 dih10 ofe2 2.371600 ofe3 2.371600 ofeo3 109.471 ofe4 2.371600 ofeo4 109.471 dih4 120.000 xxfe5 2.000000 S 19 0.05 xxfeo5 109.471 dih5 -120.000 ho6 0.947000 hofe6 109.471 dih6 180.000 ho7 0.947000 hofe7 109.471 dih7 0.000 ho8 0.947000 hofe8 109.471 dih8 -180.000 hxx9 0.370000 f hxxfe9 90.000 f dih9 180.000 f hxx10 0.370000 f hxxfe10 90.000 f dih10 180.000 f Dr. Joshua Layfield Assistant Professor, Department of Chemistry University of St. Thomas Maill # OSS 402 2115 Summit Ave. St. Paul, MN 55105-1079 (651) 962-5577 On 3/24/15, 12:00 PM, "Safiya Ess Amer amersaf85]~[yahoo.com" wrote: > >Sent to CCL by: "Safiya Ess Amer" [amersaf85||yahoo.com] >Hello. >Please, how can I use ghost atom with Cartesian coordinates? >I have system of H2-Fe(OH)3 and use G03W for getting energy as function >of >more distances (Z) from center of H2 to Fe atom. I am calculating now >each >value of energy at some distance manually. I need to put ghost atom at >center >of H2, how can I do that to get PES. > >Can anyone help me in input file? >I have geometry of the system. > >Thanks in advance > >Safiya Amer >amersaf85]^[yahoo.com> > From owner-chemistry@ccl.net Tue Mar 24 20:45:01 2015 From: "Robert Molt r.molt.chemical.physics#gmail.com" To: CCL Subject: CCL:G: Gaussian IR frequency calculation Message-Id: <-51193-150324185350-19126-Ri6zjn5M0SHUVO9SFxrgDg---server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 24 Mar 2015 18:53:41 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics*|*gmail.com] The issue is not whether it's 3%, the issue is the source, to me. You claim the error is anharmonicity. What evidence is there of that? For a molecule with very small modes (say, a protein), we are going to be down to 10 inverse centimeter modes. Those will be heavily anharmonically dominated. That can be a single-reference organic molecule, it's just big, and coupling of modes occurs. By contrast, a molecule which is significantly multi-reference will have its error having nothing to do with anharmonicity, but because multi-reference wavefunctions are often completely wrong when treated by KS-DFT (and many other methods). On 3/24/15 1:03 PM, Abrash, Samuel sabrash- -richmond.edu wrote: > Sent to CCL by: "Abrash, Samuel" [sabrash ~~ richmond.edu] > So I think the data that Robert just cited supports my claim of a 3% error. In the range 4000 cm-1 to 400 cm-1, the mid-ir, a 3% error would range from 120 cm-1 to 12 cm-1 so a 31 cm-1 average seems to be a bit below 3%. The other support for my claim is to go to the CCCDB (I think that's the correct number of C's) hosted at NIST, and check out the correction factors. For the types of high quality functional/basis set combinations, the correction factors are greater than .97, again consistent with an error of ~3%. > > Samuel A. Abrash > Associate Professor, Department of Chemistry > Coordinator, Environmental Studies Program > University of Richmond > sabrash~!~richmond.edu > Cell: (804) 363-2597 > www.richmond.edu/~sabrash > “At the time God created the world and desired to reveal the depth of His being from out of the hidden, the light came from darkness and they were joined together. Because of this, out of darkness came the light, and out of the hidden came the revealed and out of the good came evil and out of mercy came severe judgement, and everything is intertwined with everything else… the good inclination and the evil inclination, the right and the left.” The Zohar > > -----Original Message----- >> From: owner-chemistry+sabrash==richmond.edu~!~ccl.net [mailto:owner-chemistry+sabrash==richmond.edu~!~ccl.net] On Behalf Of Robert Molt r.molt.chemical.physics ~ gmail.com > Sent: Monday, March 23, 2015 10:58 PM > To: Abrash, Samuel > Subject: CCL:G: Gaussian IR frequency calculation > > > Sent to CCL by: Robert Molt [r.molt.chemical.physics]![gmail.com] > I respectfully disagree with the claim that KS-DFT functionals get 97% accuracy of the correct value, and the remaining 3% is mostly anharmonic. That assumes that KS-DFT functionals are describing electron correlation perfectly, as opposed to it being an approximate method varying in semi-empirical character from none to high. > > The mean absolute error over the G2 set of vibrational frequencies of B3LYP is 31 wavenumbers (see the 1998 paper from Adamo and Barone), obviously weighted more heavily for the higher values frequencies statistically. The RMS error can be as high as 42 wavenumbers (1993 Pople paper). > > The first harmonic mode of many molecules is often small, and the percent error is much higher on this first mode (independent of harmonic vs. anharmonic). > > On 3/23/15 8:51 PM, Abrash, Samuel sabrash%a%richmond.edu wrote: >> Sent to CCL by: "Abrash, Samuel" [sabrash|a|richmond.edu] With an >> appropriate functional with a good basis set, dft should get you to within about 97% of the correct value. The remainder of the error will be due to the harmonic approximation. Adding an anharmonic correction can get you to within 99%. >> >> Sent from my iPhone >> >>> On Mar 23, 2015, at 8:45 PM, zborowsk zborowsk^chemia.uj.edu.pl wrote: >>> >>> >>> Sent to CCL by: zborowsk [zborowsk^chemia.uj.edu.pl] W dniu >>> 2015-03-23 19:26, ggotelli()kaliumtech.com napisał(a): >>>> Sent to CCL by: [ggotelli[]kaliumtech.com] Thank you all for your >>>> help! >>>> I'll condense all my notes in the same mail. >>>> >>>> Krzysztof , yes I observed the difference in the whole spectrum. >>> Well, something strange. 300-400 cm-1 difference between theory and experiment around 3000 cm-1 and also around 100 cm-1?? By the way, do you have positive or negative (imaginary) frequencies around 100??? >>> >>> >>>> Serdar, the molecule that I 'm trying to calculate and where I have >>>> the differences is a dimer derived from dilactide. To estimate a >>>> scaling factor my reference molecule is dilactide in itself, which >>>> in turn has little differences between the calculated spectrum and >>>> the real one, depending on the peaks. >>>> >>>> André, thanks for the scaling factor reference. >>>> >>>> Stent, the polymer spectrum was made with an ATR device and without solvent. >>>> Because of this all calculations have done in vacuum. >>>> >>>> Robert, thanks for all your comments, they made me realize that my >>>> error was trying to adjust a dimer spectrum to a polymer spectrum, >>>> what are, of course, very different things. Although the dimer peaks >>>> are displaced with respect to those of the polymer, it can be seen >>>> from the GView animation that they correspond to what is expected, beyond the displacement involved. >>>> >>>> Regards! >>>> Gustavo Gotelli >>>> Polymer Synthesis >>>> Pharmaceutical Technology Department Faculty of Pharmacy and >>>> Biochemistry Buenos Aires University Argentina >>>> >>>> -----Mensaje original----- >>>> De: owner-chemistry+ggotelli==kaliumtech.com a ccl.net >>>> [mailto:owner-chemistry+ggotelli==kaliumtech.com a ccl.net] En >>>> nombre de Víctor Luaña Cabal victor^^fluor.quimica.uniovi.es Enviado >>>> el: sábado, 21 de marzo de 2015 21:16 >>>> Para: Gotelli, Gustavo A >>>> Asunto: CCL: Gaussian IR frequency calculation >>>> >>>> >>>> Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal >>>> [victor]|[fluor.quimica.uniovi.es] >>>> On Sat, Mar 21, 2015 at 05:56:44PM -0400, Robert Molt >>>> r.molt.chemical.physics],[gmail.com wrote: >>>>> Sent to CCL by: Robert Molt [r.molt.chemical.physics---gmail.com] >>>>> Moreover, you are using the B3LYP functional. It has limited >>>>> accuracy, depending on the system specifics. If it is a >>>>> multi-reference problem, great care is necessary. >>>>> >>>>> Also note that you can only compare the TOTAL spectrum, not any one peak. >>>> Robert, >>>> >>>> 1) Let me take your highly correct advise to remember to the newest >>>> generations that the role on computational chemistry is not being >>>> able to reproduce the number of the experiment. >>>> >>>> 2) The experiment helps in modulating our calculations, and the final >>>> objective is a perfect reprodution of the experiment. >>>> >>>> 3) But the reason is not substituting experiments. The reason is that >>>> in the processs of mimicking it we learn the rules that govern >>>> Nature. >>>> >>>> 4) There are too many questions in this forum that tend to ignore >>>> this rule and it is important to remember it again and again. >>>> >>>> Best regards, >>>> Dr. Víctor Luaña >>>> -- >>>> . . "The hardest part in solving a problem is recognizing >>>> / `' \ its existence. Learning the causes CAN be the road to >>>> /(o)(o)\ the solution." >>>> /`. \/ .'\ -- ¿? >>>> / '`'` \ "Lo mediocre es peor que lo bueno, pero también es peor >>>> | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es >>>> |una | '`'`| | actitud" >>>> \/`'`'`'\/ -- Jorge Wasenberg, 2015 >>>> ===(((==)))==================================+========================= >>>> ! Dr.Víctor Luaña ! Mediocre is worse than >>>> ! Departamento de Química Física y Analítica ! good, but it is also ! >>>> Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because >>>> ! e-mail: victor-#-fluor.quimica.uniovi.es ! mediocrity is not a grade, >>>> ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude >>>> +--------------------------------------------+ >>>> GroupPage : http://azufre.quimica.uniovi.es/ (being >>>> reworked)http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.c >>>> cl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- >>> https://www.youtube.com/watch?v=IGyfx3Pmeyk >>> Krzysztof K. Zborowski >>> Faculty of Chemistry >>> Jagiellonian University >>> 3 Ingardena Street >>> 30-060 Krakow >>> Poland >>> phone: +48(12)663-2067 >>> email: zborowsk(~)chemia.uj.edu.pl >>> gg 3817259 >>> skype kzys70 >>> www.chemia.uj.edu.pl/~zborowskhttp://www.ccl.net/chemistry/sub_unsub. >>> shtml> > -- > Dr. Robert Molt Jr. > r.molt.chemical.physics=-=gmail.com > Nigel Richards Research Group > Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 > 402 N. Blackford St. > Indianapolis, IN 46202http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > -- Dr. Robert Molt Jr. r.molt.chemical.physics-*-gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 From owner-chemistry@ccl.net Tue Mar 24 21:20:01 2015 From: "Yingbin Ge yingbin.ge++gmail.com" To: CCL Subject: CCL:G: Ghost atoms (symbol Bq) Message-Id: <-51194-150324195732-14864-gccLWVHxExQ0RrOUIeEBBw]![server.ccl.net> X-Original-From: Yingbin Ge Content-Type: multipart/alternative; boundary=001a1133b51e25c24f0512118bbe Date: Tue, 24 Mar 2015 16:57:21 -0700 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge^^gmail.com] --001a1133b51e25c24f0512118bbe Content-Type: text/plain; charset=UTF-8 Dear Safiya, You may find the relevant information and examples of using dummy atoms on the following web page: http://www.gaussian.com/g_tech/g_ur/c_zmat.htm Using Dummy Atoms This section will illustrate the use of dummy atoms within Z-matrices, which are represented by the pseudo atomic symbol *X*. The following example illustrates the use of a dummy atom to fix the three-fold axis in C 3v ammonia: N X 1 1. H 1 nh 2 hnx H 1 nh 2 hnx 3 120.0 H 1 nh 2 hnx 3 -120.0 nh 1.0 hnx 70.0 The position of the dummy on the axis is irrelevant, and the distance 1.0 used could have been replaced by any other positive number. *hnx* is the angle between an N-H bond and the threefold axis. Here is a Z-matrix for oxirane: X C1 X halfcc O X ox C1 90. C2 X halfcc O 90. C1 180.0 H1 C1 ch X hcc O hcco H2 C1 ch X hcc O -hcco H3 C2 ch X hcc O hcco H4 C2 ch X hcc O -hcco halfcc 0.75 ox 1.0 ch 1.08 hcc 130.0 hcco 130.0 This example illustrates two points. First, a dummy atom is placed at the center of the C-C bond to help constrain the *cco* triangle to be isosceles. *ox* is then the perpendicular distance from O to the C-C bond, and the angles *oxc* are held at 90 degrees. Second, some of the entries in the Z-matrix are represented by the negative of the dihedral angle variable *hcco*. The following examples illustrate the use of dummy atoms for specifying linear bonds. Geometry optimizations in internal coordinates are unable to handle bond angles of l80 degrees which occur in linear molecular fragments, such as acetylene or the C4 chain in butatriene. Difficulties may also be encountered in nearly linear situations such as ethynyl groups in asymmetrical molecules. These situations can be avoided by introducing dummy atoms along the angle bisector and using the half-angle as the variable or constant: N C 1 cn X 2 1. 1 90. H 2 ch 3 90. 1 180. cn 1.20 ch 1.06 Similarly, in this Z-matrix intended for a geometry optimization, *half* represents half of the N-C-O angle which is expected to be close to linear. Note that a value of *half* less than 90 degrees corresponds to a cis arrangement: N C 1 cn X 2 1. 1 half O 2 co 3 half 1 180.0 H 4 oh 2 coh 3 0.0 cn 1.20 co 1.3 oh 1.0 half 80.0 coh 105. On Tue, Mar 24, 2015 at 10:00 AM, Safiya Ess Amer amersaf85]~[yahoo.com < owner-chemistry ~~ ccl.net> wrote: > > Sent to CCL by: "Safiya Ess Amer" [amersaf85||yahoo.com] > Hello. > Please, how can I use ghost atom with Cartesian coordinates? > I have system of H2-Fe(OH)3 and use G03W for getting energy as function of > more distances (Z) from center of H2 to Fe atom. I am calculating now each > value of energy at some distance manually. I need to put ghost atom at > center > of H2, how can I do that to get PES. > > Can anyone help me in input file? > I have geometry of the system. > > Thanks in advance > > Safiya Amer > amersaf85]^[yahoo.com> > > -- Yingbin Ge, Associate Professor Science Building 207A Department of Chemistry Central Washington University 400 E University Way Ellensburg, WA 98926 Office Phone: 509-963-2817 --001a1133b51e25c24f0512118bbe Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Safiya,<= /span>

You may find the relevant information and exampl= es of using dummy atoms on the following web page:

= http://www.gaussian.com/g_tech/g_ur/c_zmat.htm


Using Dummy Atoms

This section will illustrate the use of dummy atoms within Z-matrices, w= hich are represented by the pseudo atomic symbol X. The following example illustrates the use of a dummy atom to= fix the three-fold axis in C3v ammonia:

N
X 1 1.
H 1 nh 2 hnx
H 1 nh 2 hnx 3  120.0
H 1 nh 2 hnx 3 -120.0
=20
nh 1.0
hnx 70.0

The position of the dummy on the axis is irrelevant, and the distance 1.0 used could have been replaced by any other positive number. hnx is the angle between an N-H bond and the th= reefold axis.

Here is a Z-matrix for oxirane:

X
C1  X halfcc
O   X     ox C1 90.
C2  X halfcc  O 90. C1 180.0
H1 C1     ch  X hcc  O  hcco
H2 C1     ch  X hcc  O -hcco
H3 C2     ch  X hcc  O  hcco
H4 C2     ch  X hcc  O -hcco
=20
halfcc   0.75
ox       1.0
ch       1.08
hcc    130.0
hcco   130.0

This example illustrates two points. First, a dummy atom is placed at th= e center of the C-C bond to help constrain the c= co triangle to be isosceles. ox is then the perpendicular distance from O to the C-C bond, and the an= gles oxc are held at 90 degrees. Second, some of the entries in the Z-matrix are represented by the negative of the dihedral angle variable hcco.

The following examples illustrate the use of dummy atoms for=20 specifying linear bonds. Geometry optimizations in internal coordinates=20 are unable to handle bond angles of l80 degrees which occur in linear=20 molecular fragments, such as acetylene or the C4 chain in=20 butatriene. Difficulties may also be encountered in nearly linear=20 situations such as ethynyl groups in asymmetrical molecules. These=20 situations can be avoided by introducing dummy atoms along the angle=20 bisector and using the half-angle as the variable or constant:

N
C 1 cn
X 2 1. 1 90.
H 2 ch 3 90. 1 180.
=20
cn 1.20
ch 1.06

Similarly, in this Z-matrix intended for a geometry optimization, half represents half of the N-C-O angle whi= ch is expected to be close to linear. Note that a value of half less than 90 degrees corresponds to a cis arra= ngement:

N
C 1 cn
X 2 1. 1 half
O 2 co 3 half 1 180.0
H 4 oh 2  coh 3   0.0
=20
cn 1.20
co 1.3
oh 1.0
half 80.0
coh 105.

On = Tue, Mar 24, 2015 at 10:00 AM, Safiya Ess Amer amersaf85]~[yahoo.com <owner-chemistry ~~ ccl.net> w= rote:

Sent to CCL by: "Safiya Ess Amer" [amersaf85||yahoo.com]
Hello.
Please, how can I use ghost atom with Cartesian coordinates?
I have system of H2-Fe(OH)3 and use G03W for getting energy as function of<= br> more distances (Z) from center of H2 to Fe atom. I am calculating now each<= br> value of energy at some distance manually. I need to put ghost atom at cent= er
of H2, how can I do that to get PES.

Can anyone help me in input file?
I have geometry of the system.

Thanks in advance

Safiya Amer
amersaf85]^[yahoo.com


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--
Yingbin Ge, Associate Professor
Science Building 207A
Department of Chemistry
Central Washington University
400 E University Way
Ellensburg, WA 98926
Office Phone: 509-963-2817
--001a1133b51e25c24f0512118bbe-- From owner-chemistry@ccl.net Tue Mar 24 23:34:01 2015 From: "Abrash, Samuel sabrash=-=richmond.edu" To: CCL Subject: CCL:G: Gaussian IR frequency calculation Message-Id: <-51195-150324225342-9921-x79Shsx3s/vXY0mgLfzaIQ-*-server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 25 Mar 2015 02:53:33 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash,richmond.edu] All points well taken. Of course, the molecule must be one that is appropriately treated by single reference methods. In addition, as you point out, macromolecules, even small proteins, will be more difficult to treat. My source for the claim that anharmonicity is the bulk of the remaining error for those systems for which KS DFT is appropriate is a paper by Benny Gerber, in which he managed for sets of small and medium sized molecules to reduce the error in anharmonically corrected vibrational spectra to 1% or less. Again, Robert, your points are well-taken. ________________________________________ > From: owner-chemistry+sabrash==richmond.edu[-]ccl.net [owner-chemistry+sabrash==richmond.edu[-]ccl.net] on behalf of Robert Molt r.molt.chemical.physics#gmail.com [owner-chemistry[-]ccl.net] Sent: Tuesday, March 24, 2015 6:53 PM To: Abrash, Samuel Subject: CCL:G: Gaussian IR frequency calculation Sent to CCL by: Robert Molt [r.molt.chemical.physics*|*gmail.com] The issue is not whether it's 3%, the issue is the source, to me. You claim the error is anharmonicity. What evidence is there of that? For a molecule with very small modes (say, a protein), we are going to be down to 10 inverse centimeter modes. Those will be heavily anharmonically dominated. That can be a single-reference organic molecule, it's just big, and coupling of modes occurs. By contrast, a molecule which is significantly multi-reference will have its error having nothing to do with anharmonicity, but because multi-reference wavefunctions are often completely wrong when treated by KS-DFT (and many other methods). On 3/24/15 1:03 PM, Abrash, Samuel sabrash- -richmond.edu wrote: > Sent to CCL by: "Abrash, Samuel" [sabrash ~~ richmond.edu] > So I think the data that Robert just cited supports my claim of a 3% error. In the range 4000 cm-1 to 400 cm-1, the mid-ir, a 3% error would range from 120 cm-1 to 12 cm-1 so a 31 cm-1 average seems to be a bit below 3%. The other support for my claim is to go to the CCCDB (I think that's the correct number of C's) hosted at NIST, and check out the correction factors. For the types of high quality functional/basis set combinations, the correction factors are greater than .97, again consistent with an error of ~3%. > > Samuel A. Abrash > Associate Professor, Department of Chemistry > Coordinator, Environmental Studies Program > University of Richmond > sabrash~!~richmond.edu > Cell: (804) 363-2597 > www.richmond.edu/~sabrash > “At the time God created the world and desired to reveal the depth of His being from out of the hidden, the light came from darkness and they were joined together. Because of this, out of darkness came the light, and out of the hidden came the revealed and out of the good came evil and out of mercy came severe judgement, and everything is intertwined with everything else… the good inclination and the evil inclination, the right and the left.” The Zohar > > -----Original Message----- >> From: owner-chemistry+sabrash==richmond.edu~!~ccl.net [mailto:owner-chemistry+sabrash==richmond.edu~!~ccl.net] On Behalf Of Robert Molt r.molt.chemical.physics ~ gmail.com > Sent: Monday, March 23, 2015 10:58 PM > To: Abrash, Samuel > Subject: CCL:G: Gaussian IR frequency calculation > > > Sent to CCL by: Robert Molt [r.molt.chemical.physics]![gmail.com] > I respectfully disagree with the claim that KS-DFT functionals get 97% accuracy of the correct value, and the remaining 3% is mostly anharmonic. That assumes that KS-DFT functionals are describing electron correlation perfectly, as opposed to it being an approximate method varying in semi-empirical character from none to high. > > The mean absolute error over the G2 set of vibrational frequencies of B3LYP is 31 wavenumbers (see the 1998 paper from Adamo and Barone), obviously weighted more heavily for the higher values frequencies statistically. The RMS error can be as high as 42 wavenumbers (1993 Pople paper). > > The first harmonic mode of many molecules is often small, and the percent error is much higher on this first mode (independent of harmonic vs. anharmonic). > > On 3/23/15 8:51 PM, Abrash, Samuel sabrash%a%richmond.edu wrote: >> Sent to CCL by: "Abrash, Samuel" [sabrash|a|richmond.edu] With an >> appropriate functional with a good basis set, dft should get you to within about 97% of the correct value. The remainder of the error will be due to the harmonic approximation. Adding an anharmonic correction can get you to within 99%. >> >> Sent from my iPhone >> >>> On Mar 23, 2015, at 8:45 PM, zborowsk zborowsk^chemia.uj.edu.pl wrote: >>> >>> >>> Sent to CCL by: zborowsk [zborowsk^chemia.uj.edu.pl] W dniu >>> 2015-03-23 19:26, ggotelli()kaliumtech.com napisał(a): >>>> Sent to CCL by: [ggotelli[]kaliumtech.com] Thank you all for your >>>> help! >>>> I'll condense all my notes in the same mail. >>>> >>>> Krzysztof , yes I observed the difference in the whole spectrum. >>> Well, something strange. 300-400 cm-1 difference between theory and experiment around 3000 cm-1 and also around 100 cm-1?? By the way, do you have positive or negative (imaginary) frequencies around 100??? >>> >>> >>>> Serdar, the molecule that I 'm trying to calculate and where I have >>>> the differences is a dimer derived from dilactide. To estimate a >>>> scaling factor my reference molecule is dilactide in itself, which >>>> in turn has little differences between the calculated spectrum and >>>> the real one, depending on the peaks. >>>> >>>> André, thanks for the scaling factor reference. >>>> >>>> Stent, the polymer spectrum was made with an ATR device and without solvent. >>>> Because of this all calculations have done in vacuum. >>>> >>>> Robert, thanks for all your comments, they made me realize that my >>>> error was trying to adjust a dimer spectrum to a polymer spectrum, >>>> what are, of course, very different things. Although the dimer peaks >>>> are displaced with respect to those of the polymer, it can be seen >>>> from the GView animation that they correspond to what is expected, beyond the displacement involved. >>>> >>>> Regards! >>>> Gustavo Gotelli >>>> Polymer Synthesis >>>> Pharmaceutical Technology Department Faculty of Pharmacy and >>>> Biochemistry Buenos Aires University Argentina >>>> >>>> -----Mensaje original----- >>>> De: owner-chemistry+ggotelli==kaliumtech.com a ccl.net >>>> [mailto:owner-chemistry+ggotelli==kaliumtech.com a ccl.net] En >>>> nombre de Víctor Luaña Cabal victor^^fluor.quimica.uniovi.es Enviado >>>> el: sábado, 21 de marzo de 2015 21:16 >>>> Para: Gotelli, Gustavo A >>>> Asunto: CCL: Gaussian IR frequency calculation >>>> >>>> >>>> Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal >>>> [victor]|[fluor.quimica.uniovi.es] >>>> On Sat, Mar 21, 2015 at 05:56:44PM -0400, Robert Molt >>>> r.molt.chemical.physics],[gmail.com wrote: >>>>> Sent to CCL by: Robert Molt [r.molt.chemical.physics---gmail.com] >>>>> Moreover, you are using the B3LYP functional. It has limited >>>>> accuracy, depending on the system specifics. If it is a >>>>> multi-reference problem, great care is necessary. >>>>> >>>>> Also note that you can only compare the TOTAL spectrum, not any one peak. >>>> Robert, >>>> >>>> 1) Let me take your highly correct advise to remember to the newest >>>> generations that the role on computational chemistry is not being >>>> able to reproduce the number of the experiment. >>>> >>>> 2) The experiment helps in modulating our calculations, and the final >>>> objective is a perfect reprodution of the experiment. >>>> >>>> 3) But the reason is not substituting experiments. The reason is that >>>> in the processs of mimicking it we learn the rules that govern >>>> Nature. >>>> >>>> 4) There are too many questions in this forum that tend to ignore >>>> this rule and it is important to remember it again and again. >>>> >>>> Best regards, >>>> Dr. Víctor Luaña >>>> -- >>>> . . "The hardest part in solving a problem is recognizing >>>> / `' \ its existence. Learning the causes CAN be the road to >>>> /(o)(o)\ the solution." >>>> /`. \/ .'\ -- ¿? >>>> / '`'` \ "Lo mediocre es peor que lo bueno, pero también es peor >>>> | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es >>>> |una | '`'`| | actitud" >>>> \/`'`'`'\/ -- Jorge Wasenberg, 2015 >>>> ===(((==)))==================================+========================= >>>> ! Dr.Víctor Luaña ! Mediocre is worse than >>>> ! Departamento de Química Física y Analítica ! good, but it is also ! >>>> Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because >>>> ! e-mail: victor-#-fluor.quimica.uniovi.es ! mediocrity is not a grade, >>>> ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude >>>> +--------------------------------------------+ >>>> GroupPage : http://azufre.quimica.uniovi.es/ (being >>>> reworked)http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.c >>>> cl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- >>> https://www.youtube.com/watch?v=IGyfx3Pmeyk >>> Krzysztof K. Zborowski >>> Faculty of Chemistry >>> Jagiellonian University >>> 3 Ingardena Street >>> 30-060 Krakow >>> Poland >>> phone: +48(12)663-2067 >>> email: zborowsk(~)chemia.uj.edu.pl >>> gg 3817259 >>> skype kzys70 >>> www.chemia.uj.edu.pl/~zborowskhttp://www.ccl.net/chemistry/sub_unsub. >>> shtml> > -- > Dr. Robert Molt Jr. > r.molt.chemical.physics=-=gmail.com > Nigel Richards Research Group > Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 > 402 N. Blackford St. > Indianapolis, IN 46202http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > -- Dr. Robert Molt Jr. r.molt.chemical.physics]^[gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt