From owner-chemistry@ccl.net Mon Apr 30 00:51:00 2007 From: "Will Lowe will_in_pc|yahoo.com" To: CCL Subject: CCL: gamess internal coord... illegal type 11 Message-Id: <-34155-070430002012-10452-4ckjb7FqCl7d0V3mq66nUQ::server.ccl.net> X-Original-From: "Will Lowe" Date: Mon, 30 Apr 2007 00:20:08 -0400 Sent to CCL by: "Will Lowe" [will_in_pc]|[yahoo.com] Dear users, I'm new to gamess and am trying to get force constants for optimized structure. I have successfully run the optimization and pasted the optimized z-matrix into the input to run the Hessian: CONTRL SCFTYP=RHF RUNTYP=HESSIAN ICHARG=0 MULT=1 COORD=ZMT NZVAR=54 END CONTRL MAXIT=75 END SYSTEM TIMLIM=999999999 MWORDS=235 END SCF DIRSCF=.TRUE. END STATPT NSTEP=1000 END BASIS GBASIS=N31 NGAUSS=6 END ELPOT IEPOT=1 WHERE=PDC END PDC PTSEL=CONNOLLY CONSTR=CHARGE END DATA ascorbate toppar C1 C O 1 1.3993695 C 2 1.4911748 1 109.3353707 C 3 1.5083526 2 102.8105937 1 0.4558029 0 C 4 1.3447000 3 110.2718397 2 -0.5401568 0 C 3 1.5288325 2 108.6056231 1 -123.6554732 0 C 6 1.5314014 3 113.7297864 2 172.2854080 0 O 7 1.4620625 6 103.6177438 3 171.2245510 0 O 6 1.4454707 3 105.7709296 2 -68.4700166 0 O 1 1.2312353 2 124.4287108 3 -179.7704008 0 O 5 1.3768209 4 126.8178161 3 179.5237568 0 O 4 1.3704297 3 119.9144041 2 178.6049028 0 H 3 1.0945449 2 106.7457350 1 119.0405695 0 H 6 1.0991831 3 108.6614051 2 50.6657410 0 H 7 1.0937666 6 111.7872871 3 -68.8319724 0 H 7 1.0980365 6 110.1003640 3 52.5684184 0 H 8 0.9758375 7 111.3198901 6 -171.5451546 0 H 9 0.9819455 6 107.0046583 3 -170.4584470 0 H 11 0.9808199 5 109.9007971 4 -178.8505208 0 H 12 0.9799619 4 111.6479499 3 -177.6398852 0 END FORCE PURIFY=.TRUE. PRTIFC=.TRUE. DECOMP=.TRUE. END ZMAT IZMAT(1)=1,1,2, 1,3,2, 1,4,3, 1,5,4, 1,6,3, 1,7,6, 1,8,7, 1,9,6, 1,10,1, 1,11,5, 1,4,12, 1,13,3, 1,14,6, 1,15,7, 1,16,7, 1,17,8, 1,18,9, 1,19,11, 1,20,12, 2,3,2,1, 2,4,3,2, 2,5,4,3, 2,6,3,2, 2,7,6,3, 2,8,7,6, 2,9,6,3, 2,10,1,2, 2,11,5,4, 2,12,4,3, 2,13,3,2, 2,14,6,3, 2,15,7,6, 2,16,7,6, 2,17,8,7, 2,18,9,6, 2,19,11,5, 2,20,12,4, 3,4,3,2,1, 3,5,4,3,2, 3,6,3,2,1, 3,7,6,3,2, 3,8,7,6,3, 3,9,6,3,2, 3,10,1,2,3, 3,11,5,4,3, 3,12,4,3,2, 3,13,3,2,1, 3,14,6,3,2, 3,15,7,6,3, 3,16,7,6,3, 3,17,8,7,6, 3,18,9,6,3, 3,19,11,5,4, 3,20,12,4,3 END I'm getting this error: INTERNAL COORD. 41 AT SUBSCRIPT 160 IS OF ILLEGAL TYPE 11 EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Sun Apr 29 22:59:43 2007 Your help is greatly appreciated. Will will_in_pc at yahoo.com From owner-chemistry@ccl.net Mon Apr 30 10:11:00 2007 From: "Shobe, David David.Shobe^^sud-chemie.com" To: CCL Subject: CCL: Vibrational frequencies with RHF and R-B3LYP - ethylene Message-Id: <-34156-070430100947-6559-Iw56941ON/e4ZauZZWH/eA()server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C78B31.1F419927" Date: Mon, 30 Apr 2007 16:09:08 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe()sud-chemie.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C78B31.1F419927 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Sriraj, =20 I can only think of two possibilities that would give you 3 negative frequencies in a molecule as small as ethylene. =20 Perhaps you are calculating some unusual structural "isomer" of ethylene such as the following: =20 H / \ H-C-C-H=20 \ / H =20 Given the unusual bonding pattern, it is not surprising that HF and B3LYP might give conflicting answers as to the number of imaginary frequencies.=20=20 =20 The other possibility I can think of is that you are trying to calculate frequencies at a non-stationary point: that is, a point where the atomic forces are not equal to zero. (The equilibrium geometry is a stationary point, as is a true transition state: at these points the forces on each atom are =3D 0, so calculating frequencies at those points are OK). The algorithm that computational chemistry programs use to calculate the frequencies assumes that the geometry is a stationary point, and that the local potential energy surface is similar to a harmonic oscillator. Thus, any frequency calculations at a non-stationary point are unreliable. =20 A consequence of this fact is that one should not optimize geometry at one level of theory and then calculate frequencies at a different level of theory. Different theoretical levels lead to slightly different equilibrium geometries, so that a geometry optimized at one level of theory IS NOT a stationary point at the other level of theory!=20=20 =20 --David Shobe =20 ________________________________ > From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net]=20 Sent: Friday, April 27, 2007 2:38 AM To: Shobe, David Subject: CCL: Vibrational frequencies with RHF and R-B3LYP - ethylene =20 if you are searching for the optimized structure of ethylene (i.e the minimum), none of the results (with 1 neg frequency or 3 negative freq) is correct. the structures u have obtained correspond to a saddle point and not the minimum.also i do not understand what u mean with a particular ethylene geometry(do u mean its anion or its cation or a specific geometry or something else). ethylene has a D2H symmetry and obviously u will obtain the optimized structure (without any imaginary frequency) with the D2H point group. now if u are looking for the transition state of ethylene the structure with the neg freq is a true transition state. the structure with the 3 neg frequency is higher order saddle point but is not the transition structure that connects two minima. hope that this will help jim "Sriraj Srinivasan ss537a/drexel.edu" wrote: Sent to CCL by: "Sriraj Srinivasan" [ss537]-[drexel.edu] Hi, I have been trying to obtain the vibrational frequency of a particular ethylene geometry, i encountered the following scenario By performing my Hessian calculations with only RHF i obtained one negative frequency, and when i did the same with R-B3LYP i got 3 negative frequencies. I was wondering if anyone could tell me why this has happened, and which of the results do i consider to be correct. I performed all my geometry optimizations with R-B3LYP. Thanks, Sriraj =20=20 This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C78B31.1F419927 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Sriraj,

 

I can only think of two possibilities = that would give you 3 negative frequencies in a molecule as small as ethylene.

 

Perhaps you are calculating some unusu= al structural “isomer” of ethylene such as the following:

 

      &n= bsp;    H

      &n= bsp;   /  \

   H—C—C—H=

      &n= bsp;   \  /

      &n= bsp;    H

 

Given the unusual bonding pattern, it = is not surprising that HF and B3LYP might give conflicting answers as to the number of imaginary frequencies. 

 

The other possibility I can think of is that you are trying to calculate frequencies at a non-stationary point: that is, a point where the atomic forces are not equal to zero.  (The equilibrium geometry is a stationary point, as is a true transition state: = at these points the forces on each atom are =3D 0, so calculating frequencies = at those points are OK).   The algorithm that computational chemistry programs use to calculate the frequencies assumes that the geometry is a stationary point, and that the local potential energy surface is similar to= a harmonic oscillator.  Thus, any frequency calculations at a non-statio= nary point are unreliable.

 

A consequence of this fact is that one should not optimize geometry at one level of theory and then calculate frequencies at a different level of theory.  Different theoretical lev= els lead to slightly different equilibrium geometries, so that a geometry optim= ized at one level of theory IS NOT a stationary point at the other level of theo= ry!  

 

--David Shobe=

 

From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net]
Sent: Friday, April 27, 2007= 2:38 AM
To: Shobe, David
Subject: CCL: Vibrational frequencies with RHF and R-B3LYP - ethylene

 

if you are searching for the optimized structure of ethylene (i.e t= he minimum), none of the results (with 1 neg frequency or 3 negative freq) is correct. the structures u have obtained correspond to a saddle point and not the minimum.also i do not understand what u mean with a particular ethylene geometry(do u mean its anion or its cation or a specific geometry or someth= ing else). ethylene has a D2H symmetry and obviously u will obtain the optimized structure (without any imaginary frequency)  with the D2H point group.=
now if u are looking for the transition state of ethylene the structure with the neg freq is a true transition state. the structure with the 3 neg frequ= ency is higher order saddle point but is not the transition structure that conne= cts two minima.

hope that this will help
jim

"Sriraj Srini= vasan ss537a/drexel.edu" <owner-chemistry{}ccl.net> wro= te:


Sent to CCL by: "Sriraj Srinivasan" [ss537]-[drexel.edu]
Hi,

I have been trying to obtain the vibrational frequency of a particular ethy= lene geometry, i encountered the following scenario

By performing my Hessian calculations with only RHF i obtained one negative frequency, and when i did the same with R-B3LYP i got 3 negative frequencie= s.

I was wondering if anyone could tell me why this has happened, and which of= the results do i consider to be correct. I performed all my geometry optimizati= ons with R-B3LYP.

Thanks,

Sriraj


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This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.
Thank you.
------_=_NextPart_001_01C78B31.1F419927-- From owner-chemistry@ccl.net Mon Apr 30 12:21:01 2007 From: "Abraham George Mankavil abraham.mankavil]=[gmail.com" To: CCL Subject: CCL: Catalysis Message-Id: <-34157-070430121807-5049-3u75LiEG5MHT0i7ESU46DA(0)server.ccl.net> X-Original-From: "Abraham George Mankavil" Date: Mon, 30 Apr 2007 12:18:03 -0400 Sent to CCL by: "Abraham George Mankavil" [abraham.mankavil{=}gmail.com] Dear All, I would like to know the best software available for modelling solid phase catalysts. Regards, Abraham George From owner-chemistry@ccl.net Mon Apr 30 14:33:01 2007 From: "Victor Bernshtein chr21vb,techunix.technion.ac.il" To: CCL Subject: CCL: Molecular Dynamics code for scattering/sputtering calculations Message-Id: <-34158-070430114930-2689-PD+CGK0Bwh32DBNRKreSAA : server.ccl.net> X-Original-From: Victor Bernshtein Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 30 Apr 2007 17:49:39 +0300 Mime-Version: 1.0 Sent to CCL by: Victor Bernshtein [chr21vb[]techunix.technion.ac.il] Dear all, I would appreciate your advice as to the information on some (preferably) free or commercial Molecular Dynamics codes that would be suitable for study of scattering, spattering, and shattering processes of non-rigid polyatomic (like, for example, fullerenes) molecule colliding with a crystal or amorphous surface. As far as I know, there is one unavailable that was developed years ago by Don E. Harrison Jr and later on extended by Roger Smith and Keith Beardmore. Thank you, Victor Sincerely yours, ----------------------------- Dr. Victor Bernshtein, Department of Chemistry. Technion-Israel Institute of Technology, Technion City, Haifa, 32000 E-mail: chr21vb(~)technion.ac.il Voice /FAX : (972)-4-829-2178 (office) ----------------------------- From owner-chemistry@ccl.net Mon Apr 30 16:13:00 2007 From: "Konstantin N Kudin konstantin_kudin*_*yahoo.com" To: CCL Subject: CCL: Quantifying environmental effects on atoms Message-Id: <-34159-070430161057-4064-J3jW+9AAre+vlJo1hdDM9w.:.server.ccl.net> X-Original-From: "Konstantin N Kudin" Date: Mon, 30 Apr 2007 16:10:54 -0400 Sent to CCL by: "Konstantin N Kudin" [konstantin_kudin : yahoo.com] Hi all, I am looking for ideas on how to quantify the effects of a chemical environment on atoms. Especially those methods that provide an unambiguous partitioning into atomic contributions are of interest to me. Below is a list of tools/approaches I have encountered, and if they are readily partitioned into the atomic pieces (yes/no). If you could add to this, please reply, and include the appropriate references if possible. - all kinds of charges (partitioning - yes) - electronic density differences (no) - localized orbitals (Boys, Wannier) (no) - atoms in molecules (AIM) (no?) - electron localization function (ELF) (no?) Thanks! Konstantin From owner-chemistry@ccl.net Mon Apr 30 23:53:01 2007 From: "N. Sukumar nagams\a/rpi.edu" To: CCL Subject: CCL: Quantifying environmental effects on atoms Message-Id: <-34160-070430234359-13968-SCiQN1fFY7RJCjB32AOGOw+*+server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Mon, 30 Apr 2007 22:40:18 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams*rpi.edu] One can unambiguously partition quantities that are well-defined into atomic contributions if one defines what atoms are. In AIM theory, one can partition electron density, kinetic energy, electrostatic potential, its gradient and Laplacian distribution or ANY other local functional, such as a local average ionization potential. If one does not agree on a definition of an ATOM in a molecule, NO unambiguous atomic partitioning is possible for ANY quantity ("charges" are hypothetical, generally NOT well-defined quantities... in molecular mechanics routines, for instance, these are hypothetical point charges obeying classical laws under a particular force field that is designed to reproduce some aspects of the dynamics of real molecules). Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute http://reccr.chem.rpi.edu/ ==============Original message text=============== On Mon, 30 Apr 2007 16:10:54 EDT "Konstantin N Kudin konstantin_kudin*_*yahoo.com" wrote: Sent to CCL by: "Konstantin N Kudin" [konstantin_kudin : yahoo.com] Hi all, I am looking for ideas on how to quantify the effects of a chemical environment on atoms. Especially those methods that provide an unambiguous partitioning into atomic contributions are of interest to me. Below is a list of tools/approaches I have encountered, and if they are readily partitioned into the atomic pieces (yes/no). If you could add to this, please reply, and include the appropriate references if possible. - all kinds of charges (partitioning - yes) - electronic density differences (no) - localized orbitals (Boys, Wannier) (no) - atoms in molecules (AIM) (no?) - electron localization function (ELF) (no?) Thanks! Konstantinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========