From owner-chemistry@ccl.net Sat Apr 10 03:25:00 2010 From: "Peter Khlyabich khlyabic,+,usc.edu" To: CCL Subject: CCL:G: CISAX error in TDDFT calculations Message-Id: <-41636-100410024338-23384-j7cOgrO9jvniDVVet6Fa8A---server.ccl.net> X-Original-From: "Peter Khlyabich" Date: Sat, 10 Apr 2010 02:43:37 -0400 Sent to CCL by: "Peter Khlyabich" [khlyabic~~usc.edu] Dear colleagues, I'm trying to run TDDFT calculations on Gaussian 03 software. Unfortunately i faced the error which I can't overcome. This is my input file top part: %chk=10_dtTD.chk %mem=100MW %nprocs=2 %nprocl=32 #t b3lyp td=(singlets)/6-31g(d) Int=FMMNAtoms=500 4 units 0 1 And this is the error I get after system runs for a few hours: 12 initial guesses have been made. Iteration 1 Dimension 12 NMult 12 CISAX needs 44838609 more words of memory. Error termination via Lnk1e in /usr/usc/gaussian/g03-E01/g03/linda-exe/l914.exel at Fri Apr 9 16:43:49 2010. Job cpu time: 0 days 0 hours 6 minutes 27.5 seconds. File lengths (MBytes): RWF= 15296 Int= 0 D2E= 0 Chk= 230 Scr= 1 I tried to enlarge running memory to 16g, but it didn't help. Does someone knows how I can solve this problem. Thanks in advance, Peter From owner-chemistry@ccl.net Sat Apr 10 03:59:00 2010 From: "Zhou Panwang pwzhou : gmail.com" To: CCL Subject: CCL:G: CISAX error in TDDFT calculations Message-Id: <-41637-100410035625-20068-x+6Rmy6ORdbaFLdSqYo6OQ(-)server.ccl.net> X-Original-From: Zhou Panwang Content-Type: multipart/alternative; boundary=000e0cd1a588146b540483dd3f16 Date: Sat, 10 Apr 2010 15:55:46 +0800 MIME-Version: 1.0 Sent to CCL by: Zhou Panwang [pwzhou()gmail.com] --000e0cd1a588146b540483dd3f16 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable You need more memory for your calculation=EF=BC=8C as is predicted by the e= rror message " CISAX needs 44838609 more words of memory". 2010/4/10 Peter Khlyabich khlyabic,+,usc.edu > > Sent to CCL by: "Peter Khlyabich" [khlyabic~~usc.edu] > Dear colleagues, > > I'm trying to run TDDFT calculations on Gaussian 03 software. Unfortunate= ly > i faced the error which I can't overcome. > > This is my input file top part: > > %chk=3D10_dtTD.chk > %mem=3D100MW > %nprocs=3D2 > %nprocl=3D32 > #t b3lyp td=3D(singlets)/6-31g(d) Int=3DFMMNAtoms=3D500 > > 4 units > > 0 1 > > And this is the error I get after system runs for a few hours: > > 12 initial guesses have been made. > Iteration 1 Dimension 12 NMult 12 > CISAX needs 44838609 more words of memory. > Error termination via Lnk1e in > /usr/usc/gaussian/g03-E01/g03/linda-exe/l914.exel at Fri Apr 9 16:43:49 > 2010. > Job cpu time: 0 days 0 hours 6 minutes 27.5 seconds. > File lengths (MBytes): RWF=3D 15296 Int=3D 0 D2E=3D 0 Chk=3D= 230 > Scr=3D 1 > > > I tried to enlarge running memory to 16g, but it didn't help. > > Does someone knows how I can solve this problem. > > Thanks in advance, > > Peter > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 =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 Panwang Zhou State Key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences. Tel: 0411-84379195 Fax: 0411-84675584 =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 --000e0cd1a588146b540483dd3f16 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable You need more memory for your calculation=EF=BC=8C as is predicted by the e= rror message " CISAX needs =C2=A044838609 more words of memory".<= br>

2010/4/10 Peter Khlyabich khlyabic,+,= usc.edu <owner-chemistry:_:ccl.net>

Sent to CCL by: "Peter =C2=A0Khlyabich" [khlyabic~~usc.edu]
Dear colleagues,

I'm trying to run TDDFT calculations on Gaussian 03 software. Unfortuna= tely i faced the error which I can't overcome.

This is my input file top part:

%chk=3D10_dtTD.chk
%mem=3D100MW
%nprocs=3D2
%nprocl=3D32
#t b3lyp td=3D(singlets)/6-31g(d) Int=3DFMMNAtoms=3D500

4 units

0 1

And this is the error I get after system runs for a few hours:

=C2=A0 =C2=A012 initial guesses have been made.
=C2=A0Iteration =C2=A0 =C2=A0 1 Dimension =C2=A0 =C2=A012 NMult =C2=A0 =C2= =A012
=C2=A0CISAX needs =C2=A044838609 more words of memory.
=C2=A0Error termination via Lnk1e in /usr/usc/gaussian/g03-E01/g03/linda-ex= e/l914.exel at Fri Apr =C2=A09 16:43:49 2010.
=C2=A0Job cpu time: =C2=A00 days =C2=A00 hours =C2=A06 minutes 27.5 seconds= .
=C2=A0File lengths (MBytes): =C2=A0RWF=3D =C2=A015296 Int=3D =C2=A0 =C2=A0 = =C2=A00 D2E=3D =C2=A0 =C2=A0 =C2=A00 Chk=3D =C2=A0 =C2=A0230 Scr=3D =C2=A0 = =C2=A0 =C2=A01


I tried to enlarge running memory to 16g, but it didn't help.

Does someone knows how I can solve this problem.

Thanks in advance,

Peter



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--
=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
Panwang Zhou
State Key Laboratory of Molecul= ar Reaction Dynamics
Dalian Institute of Chemical Physics
Chinese Aca= demy of Sciences.
Tel: 0411-84379195 Fax: 0411-84675584
=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

--000e0cd1a588146b540483dd3f16-- From owner-chemistry@ccl.net Sat Apr 10 06:15:00 2010 From: "shabbir Mohd agri_chemist(0)yahoo.com" To: CCL Subject: CCL: Decisive factors for transition energy Message-Id: <-41638-100410042610-32684-/8KgMlyzBB8q5RrHIPlmfw=server.ccl.net> X-Original-From: "shabbir Mohd" Date: Sat, 10 Apr 2010 04:26:09 -0400 Sent to CCL by: "shabbir Mohd" [agri_chemist_._yahoo.com] Dear colleagues, I am studying optical properties of a fluoro substituted borane compound. I have checked the different positions of fluoride atoms on borane cluster. I got different absorption energies for different systems. All fluoro-borane clusters have almost same LUMOs but slightly different HOMOs. Now, I am searching the factors which might cause the lowering of transition energy in some clusters. My question is that what parameters/factors can determine the transition energy in chemical systems having similar donor-acceptor strengths, pi conjugation etc? Can investigation of orbital overlap help in this regard? if yes how...? Any suggestion or reference in this regard would be highly appreciating. M.Shabbir From owner-chemistry@ccl.net Sat Apr 10 08:37:00 2010 From: "John McKelvey jmmckel===gmail.com" To: CCL Subject: CCL: CPU comparison for HF/DFT calculations in parallel Message-Id: <-41639-100410083548-31674-qPJQZTh3jhbG9rk2o3T/+w===server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 10 Apr 2010 08:35:43 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel^-^gmail.com] All, I'm looking to run DFT in an SMP environment and am wondering about what would give the fastest throughput, based on experience, dual quad Xeons, Phenom X4, i7, other multi-core cpus ... Currently have a 4 year-old dual-duel Opteron, and like it, but would like get things going 2-3times faster, or more. Many thanks, John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel_+_gmail.com From owner-chemistry@ccl.net Sat Apr 10 09:25:00 2010 From: "Masato YOSHIYA yoshiya(~)ams.eng.osaka-u.ac.jp" To: CCL Subject: CCL: Mol. mechanics or DFT Message-Id: <-41640-100410064733-20263-ziKQv31kp/J0aAD/e5swEg-#-server.ccl.net> X-Original-From: Masato YOSHIYA Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-2022-JP Date: Sat, 10 Apr 2010 19:10:47 +0900 MIME-Version: 1.0 Sent to CCL by: Masato YOSHIYA [yoshiya^ams.eng.osaka-u.ac.jp] Dear jacqueline: It's a matter of computational time, computational resources, the number of complexes you want to calculate, and interatomic potential for your complexes. If computational time and resources available to you allows, I suggest you to do it by HF or DFT calculation. If the number of complexes are too great to carry out DFT calculations or such, you need to calculate using classical molecular mechanics, provided that interatomic potential for complexes are trustworthy. If I were you, I start with DFT or such since the number of atoms in a complex is moderate and estimate how many days if not months it takes to complete all the calculations. Then, if the estimated computational time is acceptable, I'll stick to DFT or such. If not, I'll switch to classical molecular mechanics AFTER a several calculations by both DFT and classical molecular mechanics to see if the interatomic potential for the transition metal complexes are good enough for my purpose. Actually, although I'm basically a DFT guy, I often use both DFT and classical mechanics calculations when total computational time is unacceptable. In that case, after confirming the interatomic potentials for my materials are good enough for my purpose, I start with the classical ones to find more important ones to be calculated by DFT later. Good luck Best wishes, Masato jacqueline cawthray jcawth01(!)gmail.com さんは書きました: > Sent to CCL by: "jacqueline cawthray" [jcawth01|*|gmail.com] > I want to compare structures for a number of biologically relevant transition > metal complexes (< 100 atoms) and determine the factors governing the stability > such as steric strain (thermodynamic stability data is known). A collegue keeps > recommending molecular mechanics for this but given we have the resources to > carry out calculations at HF or dft level, is this the best approach? Thanks > in advance.> > From owner-chemistry@ccl.net Sat Apr 10 20:26:00 2010 From: "jaleel uc jaleel.uc:-:gmail.com" To: CCL Subject: CCL: Mol. mechanics or DFT Message-Id: <-41641-100409223603-8314-rFdwrv37CCmUMecNbYd9AQ=server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=000e0cdf16e24ee73f0483d8c5b0 Date: Sat, 10 Apr 2010 08:05:53 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc#gmail.com] --000e0cdf16e24ee73f0483d8c5b0 Content-Type: text/plain; charset=ISO-8859-1 It is better to use DFT . and for more good reference use "computational organo metallic chemistry "by author Cundary On Sat, Apr 10, 2010 at 2:57 AM, jacqueline cawthray jcawth01(!)gmail.com < owner-chemistry\a/ccl.net> wrote: > > Sent to CCL by: "jacqueline cawthray" [jcawth01|*|gmail.com] > I want to compare structures for a number of biologically relevant > transition > metal complexes (< 100 atoms) and determine the factors governing the > stability > such as steric strain (thermodynamic stability data is known). A collegue > keeps > recommending molecular mechanics for this but given we have the resources > to > carry out calculations at HF or dft level, is this the best approach? > Thanks > in advance.> > > -- Dr U.C.A.Jaleel. Asst Professor in cheminformatics Cheminformatics Division Malabar Christian College Calicut --000e0cdf16e24ee73f0483d8c5b0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable It is better to use DFT . and=A0 for more good reference use "computat= ional organo metallic chemistry "by author=A0 Cundary
On Sat, Apr 10, 2010 at 2:57 AM, jacqueline cawt= hray jcawth01(!)gmail.com <owner-chemistry\a/ccl.net> wrote:

Sent to CCL by: "jacque= line =A0cawthray" [jcawth01|*|gmail.com]
I want to compare structures for a number of biologically relevant transiti= on
metal complexes (< 100 atoms) and determine the factors governing = the stability
such as steric strain (thermodynamic stability data is kno= wn). A collegue keeps
recommending molecular mechanics for this but given we have the resources t= o
carry out calculations at HF or dft level, is this the best approach? = =A0Thanks
in advance.



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--
Dr U.C.A.Jalee= l.
Asst Professor in cheminformatics
Cheminformatics Division
Malabar C= hristian College
Calicut
--000e0cdf16e24ee73f0483d8c5b0--