G: ONIOM error -- GetSCM: Allocation for LST2 failed:

From owner-chemistry@ccl.net Wed Nov 29 04:31:00 2006 From: "Dr. Ponnadurai Ramasami ramchemi%%intnet.mu" To: CCL Subject: CCL:G: Optimisation Message-Id: <-33107-061129042603-4050-XTz9WzxO6kfx4/qX1Q42Zw=server.ccl.net> X-Original-From: "Dr. Ponnadurai Ramasami" Content-Type: multipart/alternative; boundary="----=_NextPart_000_001F_01C713BB.07C399E0" Date: Wed, 29 Nov 2006 13:34:01 +0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi^^intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_001F_01C713BB.07C399E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All I have a five membered ring, I am trying to optimise it using Gaussian = 03W. I have been able to do it at HF level with no imaginary freq. However when I use this optimised structure for a B3LYP optimisation, I = am getting one imaginary frequency. Can any suggest what is going wrong? Thanks Ramasami ------=_NextPart_000_001F_01C713BB.07C399E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear All

I have a five membered ring, I am = trying to=20 optimise it using Gaussian 03W.

I have been able to do it at HF level = with no=20 imaginary freq.

However when I use this optimised = structure for a=20 B3LYP optimisation, I am getting one imaginary frequency.

Can any suggest what is going = wrong?

Thanks

Ramasami

------=_NextPart_000_001F_01C713BB.07C399E0-- From owner-chemistry@ccl.net Wed Nov 29 05:05:00 2006 From: "Barbara Jagoda-Cwiklik barbara.cwiklik|uochb.cas.cz" To: CCL Subject: CCL:G: extra field Message-Id: <-33108-061129041220-2953-IuxatO7wohwPwQenkL4fag!^!server.ccl.net> X-Original-From: "Barbara Jagoda-Cwiklik" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 29 Nov 2006 10:12:06 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Barbara Jagoda-Cwiklik" [barbara.cwiklik##uochb.cas.cz] > Sent to CCL by: "X Yang" [xyang!=!chem.siu.edu] > HI CCLers, > I would like to study the frontier orbitals of my molecule with an external electrostatic field added to the Hamilton. Is it able to do that in Gaussian? > Thank you for your input! > Jaimee Hi Jaimee, Yes, it is - for example "Charge" keyword enables to include a charge distribution as point charges into the calculation. I hope you will find it helpful :) http://www.gaussian.com/g_ur/k_charge.htm best regards, Basia -- Barbara Jagoda-Cwiklik, Ph.D Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Prague, Czech Republic e-mail: barbara.cwiklik*o*uochb.cas.cz From owner-chemistry@ccl.net Wed Nov 29 05:40:01 2006 From: "Vincent Xianlong Wang xloongw(-)yahoo.com" To: CCL Subject: CCL:G: extra field Message-Id: <-33109-061129034808-668-ec560bvR4haebhExvjWupQ(a)server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 28 Nov 2006 23:47:44 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw()yahoo.com] Hi Jaimee Yes, you can do that in Gaussian using the Field keywords. Check the G03 manual for the usage. Here is the link to its online version, http://www.gaussian.com/g_ur/k_field.htm Best regards, Vincent --- "X Yang xyang#%#chem.siu.edu" wrote: > Sent to CCL by: "X Yang" [xyang!=!chem.siu.edu] > HI CCLers, > I would like to study the frontier orbitals of my > molecule with an > external electrostatic field added to the Hamilton. > Is it able to do > that in Gaussian? > Thank you for your input! > Jaimee > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the -,- > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST-,-ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com From owner-chemistry@ccl.net Wed Nov 29 06:15:01 2006 From: "Ramon Crehuet rcsqtc,iiqab.csic.es" To: CCL Subject: CCL:G: extra field Message-Id: <-33110-061129054621-6428-2Qergr/O4i9bYJNCuk4H3w=-=server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 29 Nov 2006 11:45:29 +0100 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc::iiqab.csic.es] Barbara Jagoda-Cwiklik barbara.cwiklik|uochb.cas.cz wrote: >Sent to CCL by: "Barbara Jagoda-Cwiklik" [barbara.cwiklik##uochb.cas.cz] > > >>Sent to CCL by: "X Yang" [xyang!=!chem.siu.edu] >>HI CCLers, >>I would like to study the frontier orbitals of my molecule with an >> >> >external electrostatic field added to the Hamilton. Is it able to do >that in Gaussian? > > >>Thank you for your input! >>Jaimee >> >> > >Hi Jaimee, >Yes, it is - for example "Charge" keyword enables to include a charge >distribution as point charges into the calculation. I hope you will find >it helpful :) >http://www.gaussian.com/g_ur/k_charge.htm > >best regards, >Basia > > > Hi Jaimee, The Field keyword may also be apropriate. http://www.gaussian.com/g_ur/k_field.htm Regards, Ramon From owner-chemistry@ccl.net Wed Nov 29 07:06:01 2006 From: "Richard Leo Wood rwoodphd(!)msn.com" To: CCL Subject: CCL: Comp versus other disciplines Message-Id: <-33111-061129070311-6424-7W38XYwnDiOJaDtfvz063w ~~ server.ccl.net> X-Original-From: "Richard Leo Wood" Date: Wed, 29 Nov 2006 07:03:10 -0500 Sent to CCL by: "Richard Leo Wood" [rwoodphd a msn.com] Hi all, In October, Dr. Allen Richon sent the message that I have pasted below to the CCL. I responded to it (not that I have left the discipline) because I wanted to see where he was going with this, but I never heard back from him. I am wondering if anyone else out there knows what came of this thread. As I recall, he told me that he was going to send me a survey to fill out, and then he was going to call me to discuss it. I would be interested to hear what became of this survey and will welcome any response. Richard Sent to CCL by: "Allen Richon" [abrichon ~ molsol.com] Hi: Would anyone who has left comp to pursue another discipline please drop me an email. I would like to have a chance to talk with you. With best regards, Allen <----------------------------------------------------> Allen B. Richon, Ph.D. Molecular Solutions, Inc. 1116 Miller Mountain Road, Suite A Saluda, NC 28773 Tel: 828-859-5038 http://www.molsol.com From owner-chemistry@ccl.net Wed Nov 29 08:54:00 2006 From: "JianBo Li pebblepeddle . gmail.com" To: CCL Subject: CCL: Frequency factor for BHandHLYP Message-Id: <-33112-061129085201-12650-kJWn53U4EtQKeaOM5hrX0A%%server.ccl.net> X-Original-From: "JianBo Li" Date: Wed, 29 Nov 2006 08:52:00 -0500 Sent to CCL by: "JianBo Li" [pebblepeddle|a|gmail.com] hi all I know there have been some optimized scaling factors for various methods with various basis sets to scale frequencies and ZPVEs and thermal corrections. You can find in http://srdata.nist.gov/cccbdb/vsf.asp But I can not find this for BHandHLYP method Does anyone have seen such papers discussed scaling factors for this method? Many thanks! From owner-chemistry@ccl.net Wed Nov 29 09:29:00 2006 From: "Wai-To Chan chan^curl.gkcl.yorku.ca" To: CCL Subject: CCL:G: Optimisation Message-Id: <-33113-061129091141-27901-zFSMSXi5lueLT8kpUE89Cw[]server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 29 Nov 2006 09:16:28 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan!A!curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<<< Dear All I have a five membered ring, I am trying to optimise it using Gaussian 03W. I have been able to do it at HF level with no imaginary freq. However when I use this optimised structure for a B3LYP optimisation, I am getting one imaginary frequency. Can any suggest what is going wrong? Thanks Ramasami >>>>>>>>>>>>>>>>>>>>>>>>>>>>> There is nothing wrong. Your geometry is a minimum stationary point at the HF level of theory. At the B3LYP level it is a maximum. To locate the minimum stationary point with B3LYP (assuming it exists) you do one of the following: If the geometry has no symmetry (C1) you simply repeat the calculation using the harmonic frequency data with options like opt=rcfc. If the geometry is symmetrical you have to distort the geometry along the direction of the normal mode associated with the imaginary frequency. Then you reoptimize the distorted geometry. You can do this manually. Or you can use a program like XVIBS. I haven't used it for some time and can't tell for sure if it will work for G03. The link to the program can be found in http://xvibs.sourceforge.net/. An idea that just crossed my mind is that you may try a one-step IRC job to distort the geometry. Never tried this myself though. Wai-To Chan From owner-chemistry@ccl.net Wed Nov 29 10:03:00 2006 From: "donna__dbkonline.com" To: CCL Subject: CCL: Comp versus other disciplines Message-Id: <-33114-061129090605-21502-9Sgg2X4IGwvJqWm9f7XmDA(~)server.ccl.net> X-Original-From: donna- -dbkonline.com Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 29 Nov 2006 08:06:47 -0600 MIME-Version: 1.0 Sent to CCL by: donna[#]dbkonline.com Quoting "Richard Leo Wood rwoodphd(!)msn.com" : > Sent to CCL by: "Richard Leo Wood" [rwoodphd a msn.com] > Hi all, > > In October, Dr. Allen Richon sent the message that I have pasted > below to the CCL. I responded to it (not that I have left the > discipline) because I wanted to see where he was going with this, > but I never heard back from him. I am wondering if anyone else out > there knows what came of this thread. As I recall, he told me that > he was going to send me a survey to fill out, and then he was going > to call me to discuss it. > > I would be interested to hear what became of this survey and will > welcome any response. I just hear from ALlen - he is still working on the survery - he just sent me a beta test of it - so I'm sure it will be coming soon ! I'm another "former" computational chemist - so I was interested as well. Donna From owner-chemistry@ccl.net Wed Nov 29 10:51:00 2006 From: "=?UTF-8?B?w5Zkw7ZuIEZhcmthcw==?= farkas-.-chem.elte.hu" To: CCL Subject: CCL:G: Optimisation Message-Id: <-33115-061129104546-13664-1J0ATu9zCQCMGWp+EdaQ+g ~ server.ccl.net> X-Original-From: =?UTF-8?B?w5Zkw7ZuIEZhcmthcw==?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 29 Nov 2006 16:46:29 +0100 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?B?w5Zkw7ZuIEZhcmthcw==?= [farkas*chem.elte.hu] Hi Ramasami It is possible the minimum at HF level is very close to a transition state at DFT level. Try Opt=Tight or if it does not help distort the molecule in the direction of the transition vector (the one which have an imaginary frequency) and re-optimize. Doing an MD simulation before re-optimizing (e.g. BOMD) may also help. If still no success, send the structure for further examination. Best wishes, )d0n Ödön Farkas Research associate professor Deparment of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas -----Original Message----- > From: owner-chemistry++ccl.net [mailto:owner-chemistry++ccl.net] Sent: Wednesday, November 29, 2006 12:04 PM To: Farkas, XdXXn Subject: CCL:G: Optimisation Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi^^intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_001F_01C713BB.07C399E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All I have a five membered ring, I am trying to optimise it using Gaussian = 03W. I have been able to do it at HF level with no imaginary freq. However when I use this optimised structure for a B3LYP optimisation, I = am getting one imaginary frequency. Can any suggest what is going wrong? Thanks Ramasami ------=_NextPart_000_001F_01C713BB.07C399E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear All

I have a five membered ring, I am = trying to=20 optimise it using Gaussian 03W.

I have been able to do it at HF level = with no=20 imaginary freq.

However when I use this optimised = structure for a=20 B3LYP optimisation, I am getting one imaginary frequency.

Can any suggest what is going = wrong?

Thanks

Ramasami

------=_NextPart_000_001F_01C713BB.07C399E0--http://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 Wed Nov 29 12:08:00 2006 From: "Gibbs, Alan C. PRDUS AGIBBS%prdus.jnj.com" To: CCL Subject: CCL:G: ONIOM error -- GetSCM: Allocation for LST2 failed: Message-Id: <-33116-061129112118-5415-Gs02Pu6aVkGz2IDVRHJkRg]~[server.ccl.net> X-Original-From: "Gibbs, Alan C. [PRDUS]" Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C713C5.71DF1BB4" Date: Wed, 29 Nov 2006 09:48:34 -0500 MIME-Version: 1.0 Sent to CCL by: "Gibbs, Alan C. [PRDUS]" [AGIBBS^-^prdus.jnj.com] This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C713C5.71DF1BB4 Content-Type: text/plain; charset="iso-8859-1" Hi CCLers, I'm having trouble with a G03 ONIOM job which dies after the following message: ... ONIOM: calculating electric field derivatives. ONIOM: Dipole =-2.32696873D+00 4.33938853D+00 2.73808494D+00 ONIOM: Dipole moment (Debye): X= -5.9146 Y= 11.0296 Z= 6.9595 Tot= 14.3202 ONIOM: Integrating ONIOM file 5 number 695 GetSCM: Allocation for LST2 failed: Core=-1707151352 Need=1090405693 GauSpace=-1707151352 MaxMem=52428800 Avail=52428800. Error termination via Lnk1e in /local//g03/l107.exe at Wed Nov 29 00:07:52 2006. Job cpu time: 0 days 13 hours 50 minutes 26.6 seconds. File lengths (MBytes): RWF= 468 Int= 0 D2E= 0 Chk= 167 Scr= 1 [route card= # opt oniom(b3lyp/6-311++g(2d,p):am1:uff) geom=connectivity scf=xqc opt=loose ] Has anyone else experienced this error? Any insight as to what is wrong is much appreciated. Al ------_=_NextPart_001_01C713C5.71DF1BB4 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable G: ONIOM error -- GetSCM: Allocation for LST2 failed:

Hi CCLers,
I'm having trouble with a G03 ONIOM job which dies = after the following message:

...
ONIOM: calculating electric field = derivatives.
ONIOM: = Dipole        =3D-2.32696873D+00 = 4.33938853D+00 2.73808494D+00
ONIOM: Dipole moment (Debye):
    X=3D    = -5.9146    Y=3D    = 11.0296    Z=3D     6.9595 = Tot=3D    14.3202
ONIOM: Integrating ONIOM file 5 = number   695
GetSCM: Allocation for LST2   = failed:
Core=3D-1707151352 Need=3D1090405693 = GauSpace=3D-1707151352 MaxMem=3D52428800 Avail=3D52428800.
Error termination via Lnk1e in = /local//g03/l107.exe at Wed Nov 29 00:07:52 2006.
Job cpu time: 0 days 13 hours 50 minutes = 26.6 seconds.
File lengths (MBytes): = RWF=3D    468 Int=3D      0 = D2E=3D      0 Chk=3D    167 = Scr=3D      1

[route card=3D # opt = oniom(b3lyp/6-311++g(2d,p):am1:uff) geom=3Dconnectivity scf=3Dxqc = opt=3Dloose ]

Has anyone else experienced this error?
Any insight as to what is wrong is much = appreciated.
Al

------_=_NextPart_001_01C713C5.71DF1BB4-- From owner-chemistry@ccl.net Wed Nov 29 14:03:00 2006 From: "Eric Scerri scerri]![chem.ucla.edu" To: CCL Subject: CCL: A philosophical question for CCL'ers Message-Id: <-33117-061129135954-14892-ETImp6Ur5gQD+z2RUdVkjA++server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-34--311453808 Date: Wed, 29 Nov 2006 11:00:23 -0800 Mime-Version: 1.0 (Apple Message framework v728) Sent to CCL by: Eric Scerri [scerri###chem.ucla.edu] --Apple-Mail-34--311453808 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Popular science writers and some philosophers like to point out facts such as the following, Sodium a poisonous metal combines with chlorine, a greenish poisonous gas, to yield something that is not only non-poisonous but essential for life - NaCl. or that an explosive element like hydrogen combines with oxygen, the element that is essential for combustion, to produce a compound that puts out fires - H2O. My question is, to what extent can the resulting properties of compounds be predicted ab initio from current physical theory from a knowledge of the properties of the contributing elements? Please feel free to stray from these questions since they may be loaded by referring to properties that are not so accessible to physical theory, namely being poisonous or not, or being able to extinguish fires. Secondly can current physical theory predict which particular compound, let's say its formula, will be formed from any two particular elements in the periodic table given the identity of the elements and the conditions under which the reaction is to be carried out? Or is it just the case that theory typically predicts the possible compounds that might form? And once one knows the identity of the compound presumably things look better and better for the reductionist since one can now predict bond angles, dipole, bond lengths, energies etc to any required level of accuracy? regards, eric scerri ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------- The Periodic Table: Its Story and Its Significance, by Eric Scerri, Oxford University Press, 2006. ------------------------------------------------------------------------ ------------------------------------------------------------------------ --------------------------------------------- Dr. Eric Scerri Department of Chemistry & Biochemistry, Charles Young Drive, Los Angeles, CA 90095. 310 206 7443 fax: 310 206 2061 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 00.html International Society for the Philosophy of Chemistry, http://ispc.sas.upenn.edu/ --Apple-Mail-34--311453808 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

Popular science writers and some = philosophers like to point out facts such as the following,

Sodium a poisonous metal = combines with chlorine, a greenish poisonous gas, to yield something = that is not only non-poisonous but essential for life - = NaCl.

or that an explosive element like hydrogen combines with = oxygen, the element that is essential for combustion, to produce a = compound that puts out fires - H2O.

My question is, to what = extent can the resulting properties of compounds be predicted ab initio = > from current physical theory from a knowledge of the properties of the = contributing elements?

Please feel free to stray = > from these questions since they may be loaded by referring to properties = that are not so accessible to physical theory, namely being poisonous or = not, or being able to extinguish fires.

Secondly can current = physical theory predict which particular compound, let's say its = formula, will be formed from any two particular elements in the periodic = table given the identity of the elements and the conditions under which = the reaction is to be carried out?=A0=A0

Or is it just the case that = theory typically predicts the possible compounds that might = form?

And once one knows the = identity of the compound presumably things look better and better for = the reductionist since one can now predict bond angles, dipole, bond = lengths, energies etc to any required level of accuracy?

regards,

eric = scerri

The Periodic Table: Its = Story and Its Significance, by Eric Scerri, Oxford University Press, = 2006.
-----------------------------------------------------------------= --------------------------------------------------------------------------= --------------------------------------------------

Dr. Eric Scerri

Department of Chemistry & = Biochemistry,

Charles Young = Drive,

Los = Angeles,

CA = 90095.

310 206 7443

fax: 310 206 2061

UCLA faculty web page:=A0=A0=A0http://www.chem.ucla.edu/dept/Faculty/scerri/

Editor of Foundations of Chemistry,

http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-3554= 5882-detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles= ,00.html

International Society for the Philosophy of = Chemistry,

http://ispc.sas.upenn.edu/

<= /SPAN>

= --Apple-Mail-34--311453808-- From owner-chemistry@ccl.net Wed Nov 29 16:50:01 2006 From: "Shobe, David David.Shobe]|[sud-chemie.com" To: CCL Subject: CCL: A philosophical question for CCL'ers Message-Id: <-33118-061129164054-20413-EfSnuIES4i4+8Elo/U4gZg ~ server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 29 Nov 2006 22:40:36 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe*o*sud-chemie.com] Eric Scerri wrote: > Sodium a poisonous metal combines with chlorine, a greenish poisonous gas, > to yield something that is not only non-poisonous but essential for life - NaCl. > or that an explosive element like hydrogen combines with oxygen, the element that > is essential for combustion, to produce a compound that puts out fires - H2O. Eric, In both these cases, we have reactive elements combining to form products which are less reactive...and there is the thermodynamic argument of why this should normally be the case. (OTOH there are some counterexamples, like the mercury azides HgN6 and Hg2N6!) As to predicting properties of compounds, we may have to make a distinction. The predictions of computational chemistry are based on simulations, i.e. solving complicated sets of equations; these predictions are can be made to an arbitrary level of accuracy, but don't in themselves provide any insight as to why a compound has a given property. Then there are predictions based on causes and effects we can understand. It's one thing to be able to predict the geometries and cohesion energies of a water cluster by running a simulation, and another thing to predict them using one's knowledge of hydrogen bonds. I've come across the term epiphenomenon, meaning a phenomenon of a system which consists of a collection of subsystems, but which is not easily predicted from a (however detailed it may be) knowledge of the subsystems. The properties of solids and molecules are epiphenomena of the properties of atoms, which are in turn epiphenomena of the properties of positive integers. The acknowledgement that epiphenomena are common in natural systems provides a middle ground in the holism-reductionism debate: one can make a simulation-based prediction by considering the system by reducing it to a sum of its parts, but one cannot always make an understanding-based prediction of the system. Regards, --David Shobe S�d-Chemie, Inc. P.S. I would be interested in knowing the correct terms for what I called a simulation-based prediction and an understanding-based prediction. -----Original Message----- > From: owner-chemistry*ccl.net [mailto:owner-chemistry*ccl.net] Sent: Wednesday, November 29, 2006 2:04 PM To: Shobe, David Subject: CCL: A philosophical question for CCL'ers Sent to CCL by: Eric Scerri [scerri###chem.ucla.edu] --Apple-Mail-34--311453808 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Popular science writers and some philosophers like to point out facts such as the following, Sodium a poisonous metal combines with chlorine, a greenish poisonous gas, to yield something that is not only non-poisonous but essential for life - NaCl. or that an explosive element like hydrogen combines with oxygen, the element that is essential for combustion, to produce a compound that puts out fires - H2O. My question is, to what extent can the resulting properties of compounds be predicted ab initio from current physical theory from a knowledge of the properties of the contributing elements? Please feel free to stray from these questions since they may be loaded by referring to properties that are not so accessible to physical theory, namely being poisonous or not, or being able to extinguish fires. Secondly can current physical theory predict which particular compound, let's say its formula, will be formed from any two particular elements in the periodic table given the identity of the elements and the conditions under which the reaction is to be carried out? Or is it just the case that theory typically predicts the possible compounds that might form? And once one knows the identity of the compound presumably things look better and better for the reductionist since one can now predict bond angles, dipole, bond lengths, energies etc to any required level of accuracy? regards, eric scerri ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------- The Periodic Table: Its Story and Its Significance, by Eric Scerri, Oxford University Press, 2006. ------------------------------------------------------------------------ ------------------------------------------------------------------------ --------------------------------------------- Dr. Eric Scerri Department of Chemistry & Biochemistry, Charles Young Drive, Los Angeles, CA 90095. 310 206 7443 fax: 310 206 2061 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 00.html International Society for the Philosophy of Chemistry, http://ispc.sas.upenn.edu/ --Apple-Mail-34--311453808 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

Popular science writers and some = philosophers like to point out facts such as the following,

Sodium a poisonous metal = combines with chlorine, a greenish poisonous gas, to yield something = that is not only non-poisonous but essential for life - = NaCl.

or that an explosive element like hydrogen combines with = oxygen, the element that is essential for combustion, to produce a = compound that puts out fires - H2O.

My question is, to what = extent can the resulting properties of compounds be predicted ab initio = > from current physical theory from a knowledge of the properties of the > = contributing elements?

Please feel free to stray = > from these questions since they may be loaded by referring to > properties = that are not so accessible to physical theory, namely being poisonous or = not, or being able to extinguish fires.

Or is it just the case that = theory typically predicts the possible compounds that might = form?

regards,

eric = scerri

Dr. Eric Scerri

Department of Chemistry & = Biochemistry,

Charles Young = Drive,

Los = Angeles,

CA = 90095.

310 206 7443

fax: 310 206 2061

UCLA faculty web page:=A0=A0=A0http://www.chem.ucla.edu/dept/Faculty/scerri/

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= --Apple-Mail-34--311453808--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, 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 and delete this message. Thank you. From owner-chemistry@ccl.net Wed Nov 29 17:24:00 2006 From: "Ibrahim M. Moustafa ria2(a)psu.edu" To: CCL Subject: CCL: GROMACS installation on Mac-OS Message-Id: <-33119-061129171556-27593-DhvkCYMZPYuc+pChcLNVDw(-)server.ccl.net> X-Original-From: "Ibrahim M. Moustafa" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Wed, 29 Nov 2006 17:15:38 -0500 Mime-Version: 1.0 Sent to CCL by: "Ibrahim M. Moustafa" [ria2|a|psu.edu] Hi everybody, Thanks Rick for your advice; but actually my Xcode was recently updated! I'm kind of figured out what was the problem which is: after installation and setting the variables I got an error message "Segmentation fault" when trying to issue any command...or trying the demo tutorial! It appeared that my installation was fine (even my compilation was alright......in fact compilation resulted in a code that is much faster than the provided binary for Mac-OSX). I found the whole path is required to issue GROMACS' command to run any program; although, the variable $GMXBIN is already set in my .cshrc file. This has solved the problem, but still I don't understand why I can't run the programs (e.g. pdb2gmx) by just typing "pdb2gmx" in the xterm rather than typing "$GMXBIN/pdb2gmx" to make it working!! I'm not sure if this is a an OS problem or GROMACS problem! or something obvious that I'm missing! Any advice would be appreciated. I haven't heard any comments regarding TINKER vs GROMACS as a modelling package! wish I can hear from someone though! thanks, Ibrahim At 12:22 AM 11/28/2006, you wrote: >Sent to CCL by: Rick Venable [venabler(_)nhlbi.nih.gov] >There can be issues with the gcc and g77 versions under MacOS X; in >particular, if you've kept up to date with OS patches, you may need to >download a newer version of the Xcode tools from the Apple Developer site. > >I had some problems compiling CHARMM until I updated my Xcode tools. > >-- >Rick Venable 29/500 >Membrane Biophysics Section >NIH/NHLBI Lab. of Computational Biology >Bethesda, MD 20892-8014 U.S.A. >(301) 496-1905 venabler AT nhlbi*nih*gov > > > > Sent to CCL by: "Ibrahim M. Moustafa" [ria2!=!psu.edu] > > > > I have a limited experience in Molecular modelling of protein > > structures; I'd love to expand my experience in that direction. So, I > > have few questions for people with more experience in the field. > > I wanted to install GROMACS package on my Mac-OS 10.4 according to > > the instructions on the GROMACS website. > > First, I installed the FFTW source as instructed in the README > > file. Then, I installed the GROMACS binary for the MacOS-X 10.4. > > However, it did not work! I tried the examples provided with the > > package but I got "Segmentation faults"....nothing in the output. > > Just a blank pages while the script is running interactively. > > I tried to build the package myself from the source code; but again I > > got the same error message when running the examples' scripts! > > Presumably, my installation was not successful! > > even running the command pdb2gmx gives that error message > > "Segmentation fault"!!! From owner-chemistry@ccl.net Wed Nov 29 17:59:00 2006 From: "zborowsk]_[chemia.uj.edu.pl" To: CCL Subject: CCL:G: Optimisation Message-Id: <-33120-061129094659-22042-SANcjmq3xBaRc2X0vqnvIQ#server.ccl.net> X-Original-From: zborowsk]|[chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Wed, 29 Nov 2006 15:02:59 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: zborowsk**chemia.uj.edu.pl Hi and you ring is flat?? I do not know exactly why but I observed many times that if DFT methods (especially when B3LYP is used) there is one imaginary frequency for planar structures while in HF calculations all frequencies is OK I am also want to know WHY any suggestions?? > Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi^^intnet.mu] > This is a multi-part message in MIME format. > > ------=_NextPart_000_001F_01C713BB.07C399E0 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Dear All > > I have a five membered ring, I am trying to optimise it using Gaussian = > 03W. > I have been able to do it at HF level with no imaginary freq. > However when I use this optimised structure for a B3LYP optimisation, I = > am getting one imaginary frequency. > Can any suggest what is going wrong? > > Thanks > Ramasami > > ------=_NextPart_000_001F_01C713BB.07C399E0 > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > charset=3Diso-8859-1"> > > > > >

Dear All

I have a five membered ring, I am = > trying to=20 > optimise it using Gaussian 03W.

I have been able to do it at HF level = > with no=20 > imaginary freq.

However when I use this optimised = > structure for a=20 > B3LYP optimisation, I am getting one imaginary frequency.

Can any suggest what is going = > wrong?

Thanks

Ramasami

> > ------=_NextPart_000_001F_01C713BB.07C399E0--> > > > -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk*chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70 From owner-chemistry@ccl.net Wed Nov 29 20:52:00 2006 From: "M. L. Dodson mldodson^^houston.rr.com" To: CCL Subject: CCL: GROMACS installation on Mac-OS Message-Id: <-33121-061129202307-1504-K6tbzA+jmQQZK8dJikFcNg|a|server.ccl.net> X-Original-From: "M. L. Dodson" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 29 Nov 2006 18:23:14 -0600 MIME-Version: 1.0 Sent to CCL by: "M. L. Dodson" [mldodson^houston.rr.com] On Wednesday 29 November 2006 16:30, Ibrahim M. Moustafa ria2(a)psu.edu wrote: > Sent to CCL by: "Ibrahim M. Moustafa" [ria2|a|psu.edu] > Hi everybody, > > Thanks Rick for your advice; but actually my Xcode was recently > updated! I'm kind of figured out what was the problem which is: after > installation and setting the variables I got an error message > "Segmentation fault" when trying to issue any command...or trying the > demo tutorial! > It appeared that my installation was fine (even my compilation was > alright......in fact compilation resulted in a code that is much > faster than the provided binary for Mac-OSX). > I found the whole path is required to issue GROMACS' command to run > any program; although, the variable $GMXBIN is already set in my > .cshrc file. This has solved the problem, but still I don't > understand why I can't run the programs (e.g. pdb2gmx) by just typing > "pdb2gmx" in the xterm rather than typing "$GMXBIN/pdb2gmx" to make > it working!! I'm not sure if this is a an OS problem or GROMACS > problem! or something obvious that I'm missing! Any advice would be > appreciated. > > I haven't heard any comments regarding TINKER vs GROMACS as a > modelling package! wish I can hear from someone though! > > thanks, > Ibrahim Try issuing the command printenv PATH and look to see if the $GMXBIN directory is in your path. The behavior you describe indicates it is probably not there. Fix your .cshrc to include it, and your "full path problem" should go away. The seg fault problem may indicate that your have some component(s) compiled for single precision and other components compiled for double precision. On FreeBSD (at least on Intel architectures), this can be confusing at times. GROMACS gets a lot of its speed by running in single precision, whereas most other MD packages are compiled for double precision. In particular, make sure the compiled precisions match for your GROMACS and FFTW installations. As to your TINKER vs GROMACS question, I prefer AMBER and namd :-) Bud Dodson > > At 12:22 AM 11/28/2006, you wrote: > >Sent to CCL by: Rick Venable [venabler(_)nhlbi.nih.gov] > >There can be issues with the gcc and g77 versions under MacOS X; in > >particular, if you've kept up to date with OS patches, you may need to > >download a newer version of the Xcode tools from the Apple Developer > > site. > > > >I had some problems compiling CHARMM until I updated my Xcode tools. > > > >-- > >Rick Venable 29/500 > >Membrane Biophysics Section > >NIH/NHLBI Lab. of Computational Biology > >Bethesda, MD 20892-8014 U.S.A. > >(301) 496-1905 venabler AT nhlbi*nih*gov > > > > > Sent to CCL by: "Ibrahim M. Moustafa" [ria2!=!psu.edu] > > > > > > I have a limited experience in Molecular modelling of protein > > > structures; I'd love to expand my experience in that direction. So, I > > > have few questions for people with more experience in the field. > > > I wanted to install GROMACS package on my Mac-OS 10.4 according to > > > the instructions on the GROMACS website. > > > First, I installed the FFTW source as instructed in the README > > > file. Then, I installed the GROMACS binary for the MacOS-X 10.4. > > > However, it did not work! I tried the examples provided with the > > > package but I got "Segmentation faults"....nothing in the output. > > > Just a blank pages while the script is running interactively. > > > I tried to build the package myself from the source code; but again I > > > got the same error message when running the examples' scripts! > > > Presumably, my installation was not successful! > > > even running the command pdb2gmx gives that error message > > > "Segmentation fault"!!!-- M. L. Dodson Email: mldodson-at-houston-dot-rr-dot-com Phone: eight_three_two-56_three-386_one From owner-chemistry@ccl.net Wed Nov 29 22:19:01 2006 From: "Adil Zhugralin zhugrali * bc.edu" To: CCL Subject: CCL:G: NBO visualization with GaussView Message-Id: <-33122-061129221709-14017-8y1/taWEwLu+kXS5+pwLug.@.server.ccl.net> X-Original-From: "Adil Zhugralin" Date: Wed, 29 Nov 2006 22:17:09 -0500 Sent to CCL by: "Adil Zhugralin" [zhugrali:_:bc.edu] Dear CCL'ers, I don't seem to be able to generate MO's from .chk file in GaussView. I load .log file (calculation done on G03), open MO Editor, check "read checkpoint file" in Guess type and try to load the .chk file after specifying the path to it; however, gv responds with an error message: CConnectionGFCHK::Initialize() Cannot find file What does this error mean? How can I fix it? Any suggestions would be appreciated. Thank you very much in advance. Adil BC