From owner-chemistry@ccl.net Fri Jan 9 01:24:00 2015 From: "Visvaldas K. coyote_v2002-$-yahoo.com" To: CCL Subject: CCL: Molecular orbital Message-Id: <-50880-150109012124-26842-t3IGrCKg+XynCBZxeaGyeQ[a]server.ccl.net> X-Original-From: "Visvaldas K." Content-Type: multipart/alternative; boundary="----=_Part_77744_1435161117.1420784468289" Date: Fri, 9 Jan 2015 06:21:08 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: "Visvaldas K." [coyote_v2002*yahoo.com] ------=_Part_77744_1435161117.1420784468289 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Partha, I couldn't resist:=C2=A0 the answer is actually a bit funny: yes it is, for= example sigma antibonding orbital of the CORE shell (1s) of O2 is lower th= an any orbital of 2nd shell, including even bonding orbitals. As for second= shell, I am not sure, but stranger things have happened:) Cheers, Vis From: Partha Sengupta anapspsmo%a%gmail.com To: "Kairys, Visvaldas " =20 Sent: Friday, January 9, 2015 6:15 AM Subject: CCL: Molecular orbital =20 Friends, Is it possible that antibonding sigma orbital (sigma*) has lower e= nergy (stable compared to pi*) than pi antibonding orbital? Partha=20 --=20 Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan ------=_Part_77744_1435161117.1420784468289 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Partha,

I couldn'= t resist:  the answer is actually a bit funny: yes it is, for example = sigma antibonding orbital of the CORE shell (1s) of O2 is lower than any or= bital of 2nd shell, including even bonding orbitals. As for second shell, I= am not sure, but stranger things have happened:)

Cheers,<= /div>

Vis

From: Partha Sengup= ta anapspsmo%a%gmail.com <owner-chemistry~~ccl.net>
To: "Kairys, Visvaldas " <coyo= te_v2002~~yahoo.com>
Sent: Friday, January 9, 2015 6:15 AM
Subject: CCL: Molecular orbital

Friends, Is it possible that= antibonding sigma orbital (sigma*) has lower energy (stable compared to pi= *) than pi antibonding orbital?
Partha

--
Dr. Partha Sarathi Sengupta
Associate Profes= sor
Vivekananda Mahavidyalaya, Burdwan


------=_Part_77744_1435161117.1420784468289-- From owner-chemistry@ccl.net Fri Jan 9 02:06:01 2015 From: "niveditha reddy s nivs916_._gmail.com" To: CCL Subject: CCL: error in internal co-ordinate system in Message-Id: <-50881-150109020405-31415-2Z2evf40bvRHciCvbCNepA::server.ccl.net> X-Original-From: "niveditha reddy s" Date: Fri, 9 Jan 2015 02:03:57 -0500 Sent to CCL by: "niveditha reddy s" [nivs916]-[gmail.com] Dear all, i'm performing transition state optimization using qst3 method. suprisingly, even though i have mentioned cartesian key word, it is giving error in internal co-ordinate system. i have also tried giving input in z-matrix format, with cartesian keyword which is also resulting in the same error. here is my input file. %mem=2000MB %chk=step5reactant.chk #p opt(cartesian,qst3,loose,maxcycle=400,calcfc) hf/3-21g scf(convergence=5) nosym freq=noraman Title Card 0 2 C 1.35304070 4.83278814 0.86817857 geometry specifation follows...... and last few lines of my out put file are... GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Eigenvalue 121 is 1.19D-06 should be less than 0.000000 Eigenvector: R3 R2 R49 R1 R46 1 0.63524 0.42437 -0.40049 0.21753 -0.21679 A1 A16 R50 R45 A3 1 -0.14879 0.11945 -0.11407 0.11045 0.10781 Eigenvalue 122 is 2.86D-07 should be less than 0.000000 Eigenvector: R2 A2 A1 R3 R49 1 0.42545 -0.42004 0.27879 -0.26774 -0.23335 A84 A4 R46 A86 A5 1 0.20585 -0.18463 0.17368 -0.16554 0.13986 Eigenvalue 123 is 1.23D-07 should be less than 0.000000 Eigenvector: D116 D118 R29 R30 D113 1 0.49110 -0.49006 -0.30785 -0.24885 0.14796 R32 R20 R68 R19 R46 1 -0.14652 0.13293 0.12573 -0.12553 0.12380 NTrRot= -1 NTRed= 562 NAtoms= 42 NSkip= 442 IsLin=F Error in internal coordinate system. Error termination via Lnk1e in /opt/Apps/g09/l103.exe at Tue Aug 26 15:40:11 2014. Job cpu time: 0 days 0 hours 0 minutes 58.2 seconds. File lengths (MBytes): RWF= 536 Int= 0 D2E= 0 Chk= 11 Scr= 1 i,m unable to understand why it is taking internal cordinates, even though i have mentioned cartesian co-ordinates. if any one have the explanation for this problem, please help me out. thanks in advance. From owner-chemistry@ccl.net Fri Jan 9 08:00:01 2015 From: "Henrique Junior henriquecsj]~[gmail.com" To: CCL Subject: CCL: NWChem x ORCA - Pros and cons? Message-Id: <-50882-150109075818-28499-WD0jZwY/6s5Fx0ZPoiEPeg{=}server.ccl.net> X-Original-From: Henrique Junior Content-Type: multipart/alternative; boundary=089e0111c0589989fc050c37b531 Date: Fri, 9 Jan 2015 10:57:32 -0200 MIME-Version: 1.0 Sent to CCL by: Henrique Junior [henriquecsj\a/gmail.com] --089e0111c0589989fc050c37b531 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear coleagues, I'd like to know what you think about this two softwares, NWChem and ORCA. What are the pros and cons, in your opinion? --=20 *Henrique C. S. Junior* Qu=C3=ADmica Industrial - UFRRJ Centro de Processamento de Dados - PMP --089e0111c0589989fc050c37b531 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
=09 =09 =09 =09

Dear coleagues, I'd like to know what you think about this two softwares, NWChem and ORCA. What are the pros and cons, in your opinion?



--
Henrique C. S. J= unior
Qu=C3=ADmica Industrial - UFRRJ
Centro de Processame= nto de Dados - PMP
--089e0111c0589989fc050c37b531-- From owner-chemistry@ccl.net Fri Jan 9 10:01:01 2015 From: "Zork Zou zorkzou(-)gmail.com" To: CCL Subject: CCL:G: error in internal co-ordinate system in Message-Id: <-50883-150109093920-26270-LsIH1fyhEAZQHOwO/iPUmg*server.ccl.net> X-Original-From: Zork Zou Content-Type: multipart/alternative; boundary=001a11c24edaea3ae6050c391e34 Date: Fri, 9 Jan 2015 08:39:14 -0600 MIME-Version: 1.0 Sent to CCL by: Zork Zou [zorkzou() gmail.com] --001a11c24edaea3ae6050c391e34 Content-Type: text/plain; charset=UTF-8 Dear Niveditha, The reason may be that Gaussian is not clever enough to find all the weak bonds (and the related angles) in a big molecule. OPT(Cartesian) may solve this problem, but some kinds of OPT calculation were programmed only in redundant coordinates. Please check whether there are some important weak bonds missing in the table of redundant coordinates. For example, long hydrogen bonds which exceed internal threshold. If so, add an option OPT(ModRedundant) and specify those bonds in the format atom-1 atom-2 B Since the problematic molecules are often large (number of atoms from 50 to 1000+), it's better to write a program to search the missing bonds. Best regards, Wenli On Fri, Jan 9, 2015 at 1:03 AM, niveditha reddy s nivs916_._gmail.com < owner-chemistry]-[ccl.net> wrote: > > Sent to CCL by: "niveditha reddy s" [nivs916]-[gmail.com] > Dear all, > i'm performing transition state optimization using qst3 method. > suprisingly, > even though i have mentioned cartesian key word, it is giving error in > internal co-ordinate system. i have also tried giving input in z-matrix > format, with cartesian keyword which is also resulting in the same error. > here is my input file. > > %mem=2000MB > %chk=step5reactant.chk > #p opt(cartesian,qst3,loose,maxcycle=400,calcfc) hf/3-21g > scf(convergence=5) > nosym freq=noraman > > Title Card > > 0 2 > C 1.35304070 4.83278814 0.86817857 > geometry specifation follows...... > > > and last few lines of my out put file are... > > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > Berny optimization. > Eigenvalue 121 is 1.19D-06 should be less than 0.000000 > Eigenvector: > R3 R2 R49 R1 R46 > 1 0.63524 0.42437 -0.40049 0.21753 -0.21679 > A1 A16 R50 R45 A3 > 1 -0.14879 0.11945 -0.11407 0.11045 0.10781 > Eigenvalue 122 is 2.86D-07 should be less than 0.000000 > Eigenvector: > R2 A2 A1 R3 R49 > 1 0.42545 -0.42004 0.27879 -0.26774 -0.23335 > A84 A4 R46 A86 A5 > 1 0.20585 -0.18463 0.17368 -0.16554 0.13986 > Eigenvalue 123 is 1.23D-07 should be less than 0.000000 > Eigenvector: > D116 D118 R29 R30 D113 > 1 0.49110 -0.49006 -0.30785 -0.24885 0.14796 > R32 R20 R68 R19 R46 > 1 -0.14652 0.13293 0.12573 -0.12553 0.12380 > NTrRot= -1 NTRed= 562 NAtoms= 42 NSkip= 442 IsLin=F > Error in internal coordinate system. > Error termination via Lnk1e in /opt/Apps/g09/l103.exe at Tue Aug 26 > 15:40:11 > 2014. > Job cpu time: 0 days 0 hours 0 minutes 58.2 seconds. > File lengths (MBytes): RWF= 536 Int= 0 D2E= 0 Chk= 11 > Scr= > 1 > > > > > i,m unable to understand why it is taking internal cordinates, even though > i > have mentioned cartesian co-ordinates. if any one have the explanation for > this problem, please help me out. > > thanks in advance.> > > --001a11c24edaea3ae6050c391e34 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Niveditha,

The reason m= ay be that Gaussian is not clever enough to find all the weak bonds (and th= e related angles) in a big molecule.=C2=A0OPT(Cartesian) may solve this pro= blem, but some kinds of OPT calculation were programmed only in redundant c= oordinates.

Please check whether there are some im= portant weak bonds missing in the table of redundant coordinates. For examp= le, long hydrogen bonds which exceed internal threshold.=C2=A0If so, add an= option OPT(ModRedundant) and specify those bonds in the format
= =C2=A0 =C2=A0 atom-1 =C2=A0 =C2=A0atom-2 =C2=A0 B

= Since the problematic molecules are often large (number of atoms from 50 to= 1000+), it's better to write a program to search the missing bonds.

Best regards,
Wenli


On Fri, Jan 9= , 2015 at 1:03 AM, niveditha reddy s nivs916_._gmail.com <owner-chemistry]-[ccl.net> wrote:

Sent to CCL by: "niveditha reddy s" [nivs916]-[gmail.com]
Dear all,
=C2=A0i'm performing transition state optimization using qst3 method. s= uprisingly,
even though i have mentioned cartesian key word, it is giving error in
internal co-ordinate system. i have also tried giving input in z-matrix
format, with cartesian keyword which is also resulting in the same error. here is my input file.

%mem=3D2000MB
%chk=3Dstep5reactant.chk
#p opt(cartesian,qst3,loose,maxcycle=3D400,calcfc) hf/3-21g scf(convergence= =3D5)
nosym freq=3Dnoraman

Title Card

0 2
=C2=A0C=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.353= 04070=C2=A0 =C2=A0 4.83278814=C2=A0 =C2=A0 0.86817857
geometry specifation follows......


and last few lines of my out put file are...

=C2=A0GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG= rad
=C2=A0Berny optimization.
=C2=A0Eigenvalue=C2=A0 =C2=A0121 is=C2=A0 =C2=A01.19D-06 should be less tha= n=C2=A0 =C2=A0 =C2=A00.000000 Eigenvector:
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 R3=C2=A0 =C2=A0 =C2=A0 =C2=A0 R2=C2=A0 =C2=A0 =C2=A0 =C2= =A0 R49=C2=A0 =C2=A0 =C2=A0 =C2=A0R1=C2=A0 =C2=A0 =C2=A0 =C2=A0 R46
=C2=A0 =C2=A01=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 0.63524=C2=A0 =C2=A00.42437=C2=A0 -0.40049=C2=A0 =C2=A00.21753= =C2=A0 -0.21679
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 A1=C2=A0 =C2=A0 =C2=A0 =C2=A0 A16=C2=A0 =C2=A0 =C2=A0 =C2= =A0R50=C2=A0 =C2=A0 =C2=A0 =C2=A0R45=C2=A0 =C2=A0 =C2=A0 =C2=A0A3
=C2=A0 =C2=A01=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0-0.14879=C2=A0 =C2=A00.11945=C2=A0 -0.11407=C2=A0 =C2=A00.11045= =C2=A0 =C2=A00.10781
=C2=A0Eigenvalue=C2=A0 =C2=A0122 is=C2=A0 =C2=A02.86D-07 should be less tha= n=C2=A0 =C2=A0 =C2=A00.000000 Eigenvector:
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 R2=C2=A0 =C2=A0 =C2=A0 =C2=A0 A2=C2=A0 =C2=A0 =C2=A0 =C2= =A0 A1=C2=A0 =C2=A0 =C2=A0 =C2=A0 R3=C2=A0 =C2=A0 =C2=A0 =C2=A0 R49
=C2=A0 =C2=A01=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 0.42545=C2=A0 -0.42004=C2=A0 =C2=A00.27879=C2=A0 -0.26774=C2=A0 = -0.23335
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 A84=C2=A0 =C2=A0 =C2=A0 =C2=A0A4=C2=A0 =C2=A0 =C2=A0 =C2= =A0 R46=C2=A0 =C2=A0 =C2=A0 =C2=A0A86=C2=A0 =C2=A0 =C2=A0 =C2=A0A5
=C2=A0 =C2=A01=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 0.20585=C2=A0 -0.18463=C2=A0 =C2=A00.17368=C2=A0 -0.16554=C2=A0 = =C2=A00.13986
=C2=A0Eigenvalue=C2=A0 =C2=A0123 is=C2=A0 =C2=A01.23D-07 should be less tha= n=C2=A0 =C2=A0 =C2=A00.000000 Eigenvector:
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0D116=C2=A0 =C2=A0 =C2=A0 D118=C2=A0 =C2=A0 =C2=A0 =C2=A0R2= 9=C2=A0 =C2=A0 =C2=A0 =C2=A0R30=C2=A0 =C2=A0 =C2=A0 D113
=C2=A0 =C2=A01=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 0.49110=C2=A0 -0.49006=C2=A0 -0.30785=C2=A0 -0.24885=C2=A0 =C2= =A00.14796
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 R32=C2=A0 =C2=A0 =C2=A0 =C2=A0R20=C2=A0 =C2=A0 =C2=A0 =C2= =A0R68=C2=A0 =C2=A0 =C2=A0 =C2=A0R19=C2=A0 =C2=A0 =C2=A0 =C2=A0R46
=C2=A0 =C2=A01=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0-0.14652=C2=A0 =C2=A00.13293=C2=A0 =C2=A00.12573=C2=A0 -0.12553= =C2=A0 =C2=A00.12380
=C2=A0NTrRot=3D=C2=A0 =C2=A0 -1 NTRed=3D=C2=A0 =C2=A0562 NAtoms=3D=C2=A0 = =C2=A0 42 NSkip=3D=C2=A0 =C2=A0442 IsLin=3DF
=C2=A0Error in internal coordinate system.
=C2=A0Error termination via Lnk1e in /opt/Apps/g09/l103.exe at Tue Aug 26 1= 5:40:11
2014.
=C2=A0Job cpu time:=C2=A0 0 days=C2=A0 0 hours=C2=A0 0 minutes 58.2 seconds= .
=C2=A0File lengths (MBytes):=C2=A0 RWF=3D=C2=A0 =C2=A0 536 Int=3D=C2=A0 =C2= =A0 =C2=A0 0 D2E=3D=C2=A0 =C2=A0 =C2=A0 0 Chk=3D=C2=A0 =C2=A0 =C2=A011 Scr= =3D
1




i,m unable to understand why it is taking internal cordinates, even though = i
have mentioned cartesian co-ordinates. if any one have the explanation for<= br> this problem, please help me out.

=C2=A0 =C2=A0 =C2=A0thanks in advance.



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--001a11c24edaea3ae6050c391e34-- From owner-chemistry@ccl.net Fri Jan 9 22:55:00 2015 From: "Tymofii Nikolaienko tim_mail#%#ukr.net" To: CCL Subject: CCL: NWChem x ORCA - Pros and cons? Message-Id: <-50884-150109103531-9233-bc1bjNqLwMKZRKrdtZQG6w|*|server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Type: multipart/alternative; boundary="------------000607080106010703080202" Date: Fri, 09 Jan 2015 17:19:39 +0200 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail-,-ukr.net] This is a multi-part message in MIME format. --------------000607080106010703080202 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Hi! Strictly speaking, the choice depends on your task. Personally I almost always prefer ORCA due to its robustness. Moreover, since the introduction of analytical Hessian in one of its latest versions ORCA has became a real general-purpose quantum-chemical tool. Another great advantage of ORCA applicable to DFT methods is a good choice of Resolution-Of-Identity schemes. The only disadvantage I see in this package is that it does not support BSSE-corrected gradients for geometry optimization, and, less important, that they do not provide users with the binaries of the latest version for 32-bit Windows platform. On the other hand, my experience with NwChem indicates that his package can only be good if you run Linux, since the compilation of NwChem for, e.g., Cygwin (to run it under Windows) is a nightmare. My _personal_ experience is also that NwChem is much less stable if compared to ORCA - however, publications indicate that this does not prevent NwChem from being VERY widely used by researchers. Hope this helps... Best whishes Tymofii -- Tymofii Nikolaienko, Ph.D., Faculty of Physics, Taras Shevchenko National University of Kyiv (Ukraine) 09.01.2015 14:57, Henrique Junior henriquecsj]~[gmail.com wrote: > > Dear coleagues, I'd like to know what you think about this two > softwares, NWChem and ORCA. What are the pros and cons, in your opinion? > > > > -- > *Henrique C. S. Junior* > Química Industrial - UFRRJ > Centro de Processamento de Dados - PMP --------------000607080106010703080202 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit Hi!

Strictly speaking, the choice depends on your task.
Personally I almost always prefer ORCA due to its robustness.
Moreover, since the introduction of analytical Hessian in one of its latest versions ORCA has became a real general-purpose quantum-chemical tool.
Another great advantage of ORCA applicable to DFT methods is a good choice of Resolution-Of-Identity schemes.
The only disadvantage I see in this package is that it does not support BSSE-corrected gradients for geometry optimization,
and, less important, that they do not provide users with the binaries of the latest version for 32-bit Windows platform.

On the other hand, my experience with NwChem indicates that his package can only be good if you run Linux,
since the compilation of NwChem for, e.g., Cygwin (to run it under Windows) is a nightmare.
My _personal_ experience is also that NwChem is much less stable if compared to ORCA - however, publications
indicate that this does not prevent NwChem from being VERY widely used by researchers.

Hope this helps...

Best whishes
Tymofii

--
Tymofii Nikolaienko, Ph.D.,
Faculty of Physics,
Taras Shevchenko National University of Kyiv (Ukraine)





09.01.2015 14:57, Henrique Junior henriquecsj]~[gmail.com wrote:

Dear coleagues, I'd like to know what you think about this two softwares, NWChem and ORCA. What are the pros and cons, in your opinion?



--
Henrique C. S. Junior
Química Industrial - UFRRJ
Centro de Processamento de Dados - PMP
--------------000607080106010703080202--