From owner-chemistry@ccl.net Mon Sep 3 07:41:01 2007 From: "Yangsoo Kim vsmember(~)gmail.com" To: CCL Subject: CCL:G: Question: Application of Various Gas-Phase Molecules' Spectra & optical properties from Gaussian Message-Id: <-35072-070903073819-21952-/7BzTKin74NEV5YKMWU/3w(_)server.ccl.net> X-Original-From: "Yangsoo Kim" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 3 Sep 2007 20:38:23 +0900 MIME-Version: 1.0 Sent to CCL by: "Yangsoo Kim" [vsmember^^gmail.com] Dear all, As many of you already know, our computational chemistry packages can calculate various spectra & optical properties based on frequency analysis. For example, Gaussian can calculate, (1) IR, NMR, Raman & hyperfine spectra, (2) dichroism intensities, and (3) polarizabilities/hyperpolarizabilities. I wonder how those properties are used in the industry or academia & how important it would be to be able to predict those properties, especially when gas-phase molecules are considered. I believe it is important to know how our computational chemistry capability can practically be used in the real application area, but it is not very easy to find the summary of those application cases for gas-phase molecules. When we are considering, for example, the Raman or hyperfine spectra, it is extremely expensive to calculate anharmonic frequencies. Then the questions are, (1) Is it still useful to calculate the harmonic frequencies only for some real application area, or one has to calculate the anhamonic frequencies also in order to make our frequency calculations valuable in the real applicarion? (2)Which area of industry or academia will be interested in having the (an)harmonic frequency based specta? Same question could be asked for the case of dichroism intensities and polarizabilities/hyperpolarizabilities. Any comments/info about this issue would be greatly appreciated if anyone of you knows or experienced in applying those frequency based properties. I will summarize the answers. Thanks in advance, Yangsoo Kim, Ph.D. From owner-chemistry@ccl.net Mon Sep 3 10:51:00 2007 From: "Konrad Hinsen hinsen-.-cnrs-orleans.fr" To: CCL Subject: CCL: Protein Flexibility Analysis Message-Id: <-35073-070903102933-32538-R1aK4A4d99X4ldxXNJHngw*|*server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Mon, 3 Sep 2007 10:29:29 -0400 Sent to CCL by: "Konrad Hinsen" [hinsen##cnrs-orleans.fr] > Sent to CCL by: "Sina T reli" [sinatureli]|[gmail.com] > Hello, > > Do you know any software that can make protein flexibility analysis > other than M^2AP and FIRST, which I am already aware of. Please have a look at DomainFinder, available from http://dirac.cnrs-orleans.fr/DomainFinder/ - --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Molculaire, CNRS Orlans Synchrotron Soleil - Division Expriences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: hinsen],[cnrs-orleans.fr --------------------------------------------------------------------- From owner-chemistry@ccl.net Mon Sep 3 23:49:01 2007 From: "sun xy sunxy78[*]gmail.com" To: CCL Subject: CCL:G: Inaccurate quadrature in caldsu Message-Id: <-35074-070903104513-2035-ToDF8qd/JJIzbJl17rGD5w{=}server.ccl.net> X-Original-From: "sun xy" Content-Type: multipart/alternative; boundary="----=_Part_19948_8769188.1188827246075" Date: Mon, 3 Sep 2007 15:47:26 +0200 MIME-Version: 1.0 Sent to CCL by: "sun xy" [sunxy78[*]gmail.com] ------=_Part_19948_8769188.1188827246075 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All, I am trying to embedded a NaCl cluster into the point charge which around is 1000. In addition, the neighbors of clorines in the cluster has been replace with Na with ECP and you can see these in the folliwng input file, %chk=surface_10_ecp.chk %mem=5GB %nproc=4 #p HF/gen charge pseudo=read maxdisk=50gb guess(indo) scf=(maxcycle=150) ecp test 9 1 Na 0.00000000 0.00000000 0.00000000 Cl -2.84865000 0.00000000 0.00000000 Cl 2.84865000 0.00000000 0.00000000 Cl 0.00000000 2.84865000 0.00000000 Cl 0.00000000 -2.84865000 0.00000000 Cl 0.00000000 0.00000000 2.84865000 Na -2.84865000 0.00000000 2.84865000 Na 2.84865000 0.00000000 2.84865000 Na 0.00000000 2.84865000 2.84865000 Na 0.00000000 -2.84865000 2.84865000 Na -2.84865 -2.84865 0.00000 Na 2.84865 -2.84865 0.00000 Na -2.84865 2.84865 0.00000 Na 2.84865 2.84865 0.00000 Na 0.00000 -5.69730 0.00000 Na -5.69730 0.00000 0.00000 Na 5.69730 0.00000 0.00000 Na 0.00000 5.69730 0.00000 Na 0.00000 0.00000 5.69730 1,2,3,4,5,6,7,8,9,10 0 cc-pvtz **** 11,12,13,14,15,16,17,18,19 0 lanl2 -28.48650 -28.48650 0.00000 1.00 -25.63785 -28.48650 0.00000 -1.00 -22.78920 -28.48650 0.00000 1.00 -19.94055 -28.48650 0.00000 -1.00 -17.09190 -28.48650 0.00000 1.00 -14.24325 -28.48650 0.00000 -1.00 -11.39460 -28.48650 0.00000 1.00 -8.54595 -28.48650 0.00000 -1.00 -5.69730 -28.48650 0.00000 1.00 -2.84865 -28.48650 0.00000 -1.00 0.00000 -28.48650 0.00000 1.00 2.84865 -28.48650 0.00000 -1.00 5.69730 -28.48650 0.00000 1.00 8.54595 -28.48650 0.00000 -1.00 .......................... And it successfully finish SCF calculation, but get this error when it come to MP2 calculations. When I search for archive, i found mostly this error are from not so good initial guess for SCF calculation, But strange, I didn't encounter this error at SCF but when calculation coming to MP2 (I think it should already have a good HF molecular orbitals for MP2 calculations). Here are error information. SCF Done: E(RHF) = -3526.72603792 A.U. after 11 cycles Convg = 0.4061D-08 -V/T = 2.1349 S**2 = 0.0000 KE= 3.107458114335D+03 PE=-9.800532901246D+03 EE= 2.401489475020D+03 Leave Link 502 at Mon Sep 3 14:19:54 2007, MaxMem= 3355443200 cpu: 4060.8 (Enter /usr/local/Gaussian/g03/l801.exe) ExpMin= 1.50D-02 ExpMax= 4.56D+05 ExpMxC= 1.00D+04 IAcc=3 IRadAn= 5 AccDes= 0.00D+00 HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 5 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 Spurious integrated density or basis function: NE= 239 NElCor= 0 El error=6.88D+01 rel=2.88D-01 Tolerance=1.00D-03 Shell 121 absolute error=7.78D-06 Tolerance=1.20D-02 Shell 121 signed error=7.78D-06 Tolerance=1.00D-01 Inaccurate quadrature in CalDSu. Error termination via Lnk1e in /usr/local/Gaussian/g03/l801.exe at Mon Sep 3 14:20:12 2007. Job cpu time: 0 days 1 hours 9 minutes 59.7 seconds. File lengths (MBytes): RWF= 57 Int= 0 D2E= 0 Chk= 16 Scr= 1 ------=_Part_19948_8769188.1188827246075 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All,

    I am trying to embedded a NaCl cluster into the point charge which around is 1000. In addition, the neighbors of clorines in the cluster has been replace with Na with ECP and you can see these in the folliwng input file,

%chk=surface_10_ecp.chk
%mem=5GB
%nproc=4
#p HF/gen charge pseudo=read maxdisk=50gb guess(indo)
scf=(maxcycle=150)
 
ecp test

9 1
 Na                 0.00000000    0.00000000    0.00000000
 Cl                -2.84865000    0.00000000    0.00000000
 Cl                 2.84865000    0.00000000    0.00000000
 Cl                 0.00000000    2.84865000    0.00000000
 Cl                 0.00000000   - 2.84865000    0.00000000
 Cl                 0.00000000    0.00000000    2.84865000
 Na                -2.84865000    0.00000000    2.84865000
 Na                 2.84865000    0.00000000    2.84865000
 Na                 0.00000000    2.84865000    2.84865000
 Na                 0.00000000   -2.84865000    2.84865000
 Na      -2.84865    -2.84865     0.00000
 Na       2.84865    -2.84865     0.00000
 Na      -2.84865     2.84865      0.00000
 Na       2.84865     2.84865     0.00000
 Na       0.00000    -5.69730     0.00000
 Na      -5.69730     0.00000     0.00000
 Na       5.69730     0.00000     0.00000
 Na       0.00000     5.69730      0.00000
 Na       0.00000     0.00000     5.69730

1,2,3,4,5,6,7,8,9,10 0
 cc-pvtz
****

11,12,13,14,15,16,17,18,19 0
lanl2

    -28.48650  -28.48650    0.00000   1.00
    -25.63785  - 28.48650    0.00000  -1.00
    -22.78920  -28.48650    0.00000   1.00
    -19.94055  -28.48650    0.00000  -1.00
    -17.09190  -28.48650    0.00000   1.00
    -14.24325  -28.48650    0.00000  -1.00
    -11.39460   -28.48650    0.00000   1.00
     -8.54595  -28.48650    0.00000  -1.00
     -5.69730  -28.48650    0.00000   1.00
     -2.84865  -28.48650    0.00000  -1.00
      0.00000  -28.48650    0.00000   1.00
      2.84865  -28.48650    0.00000  -1.00
      5.69730  -28.48650    0.00000   1.00
      8.54595  -28.48650    0.00000  -1.00
..........................


And it successfully finish SCF calculation, but get this error when it come to MP2 calculations. When I search for archive, i found mostly this error are from not so good initial guess for SCF calculation, But strange, I didn't encounter this error at SCF but when calculation coming to MP2 (I think it should already have a good HF molecular orbitals for MP2 calculations). Here are error information.


 SCF Done:  E(RHF) =  -3526.72603792     A.U. after   11 cycles
             Convg  =    0.4061D-08             -V/T =  2.1349
             S**2   =   0.0000
 KE= 3.107458114335D+03 PE=-9.800532901246D+03 EE= 2.401489475020D+03
 Leave Link  502 at Mon Sep  3 14:19:54 2007, MaxMem= 3355443200 cpu:    4060.8
 (Enter /usr/local/Gaussian/g03/l801.exe)
 ExpMin= 1.50D-02 ExpMax= 4.56D+05 ExpMxC= 1.00D+04 IAcc=3 IRadAn=         5 AccDes= 0.00D+00
 HarFok:  IExCor= 205 AccDes= 0.00D+00 IRadAn=         5 IDoV=1
 ScaDFX=  1.000000  1.000000  1.000000  1.000000
 Spurious integrated density or basis function:
 NE=  239 NElCor=    0 El error=6.88D+01 rel=2.88D-01 Tolerance=1.00D-03
 Shell   121     absolute error=7.78D-06              Tolerance=1.20D-02
 Shell   121       signed error=7.78D-06              Tolerance=1.00D-01
 Inaccurate quadrature in CalDSu.
 Error termination via Lnk1e in /usr/local/Gaussian/g03/l801.exe at Mon Sep  3 14:20:12 2007.
 Job cpu time:  0 days  1 hours  9 minutes 59.7 seconds.
 File lengths (MBytes):  RWF=     57 Int=      0 D2E=      0 Chk=     16 Scr=      1

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