From owner-chemistry@ccl.net Mon Nov 3 02:32:01 2008 From: "laxmikanth rao lkjoshiji,yahoo.com" To: CCL Subject: CCL:G: mail from Joshi Message-Id: <-38008-081103011511-15153-zhVDxiQdsVfV4ii5VEe1zA^-^server.ccl.net> X-Original-From: laxmikanth rao Content-Type: multipart/alternative; boundary="0-1983654453-1225689295=:56855" Date: Mon, 3 Nov 2008 10:44:55 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: laxmikanth rao [lkjoshiji!A!yahoo.com] --0-1983654453-1225689295=:56855 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear CCLers; Hi=0A=0AI am optimizing a molecule having 387 atoms (only C an= d H atoms) which includes neatly 16 methyl groups as substitutions in G03w,= and the method is b3lyp/3-21g*. During the optimization the Maximum Force = and=C2=A0RMS=C2=A0Forces are sometimes converging,=C2=A0Maximum Displacemen= t=C2=A0and=C2=A0RMS=C2=A0=C2=A0=C2=A0=C2=A0 Displacements are not convergin= g and the molecules energy is oscillating. I am using=C2=A0following keywor= ds in route section as=0A=0A%mem=3D1500mb=0A%nproc=3D4=0A#p opt=3D(gdiis,ma= xcycle=3D200) b3lyp/3-21g* scf=3Dmaxcycle=3D500 =0A=0APlease give me sugges= tion =0A=0AThanks in advance=0A=0AJoshi=0A=0A=0A=0A Add more friends t= o your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ --0-1983654453-1225689295=:56855 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear CCLers; Hi
=0A
 
=0A
I am optimizin= g a molecule having 387 atoms (only C and H atoms) which includes neatly 16= methyl groups as substitutions in G03w, and the method is b3lyp/3-21g*. Du= ring the optimization the Maximum Force and RMS Forces are someti= mes converging, Maximum Displacement and RMS  &nbs= p;  Displacements are not converging and the molecules energy is oscil= lating. I am using following keywords in route section as
=0A 
=0A
%mem=3D1500mb
%nproc=3D4
#p opt=3D(gdiis,maxcycl= e=3D200) b3lyp/3-21g* scf=3Dmaxcycle=3D500
=0A
 
=0APlease give me suggestion =0A
 
=0A
Thanks in adv= ance
=0A
 
=0A
Joshi
=0A
 
=
=0A
Add more friends to your messenger = and enjoy! Invite them now. --0-1983654453-1225689295=:56855-- From owner-chemistry@ccl.net Mon Nov 3 04:44:01 2008 From: "Kalju Kahn kalju]=[chem.ucsb.edu" To: CCL Subject: CCL:G: mail from Joshi Message-Id: <-38009-081103044157-19377-1J0ATu9zCQCMGWp+EdaQ+g!A!server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 3 Nov 2008 01:41:41 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju:+:chem.ucsb.edu] Joshi, Are you sure that you need B3LYP/3-21G* geometry for this structure? Seems like molecular mechanics with MM3 might be better suited for optimizing a large hydrocarbon. If you need DFT geometry for some reason, try to freeze all dihedrals and optimize bond distances and angles first. Small deviations of torsional angles around single bonds is more acceptable than an unusually stretched bond for calculation of some molecular properties. Kalju > Dear CCLers; Hi > > I am optimizing a molecule having 387 atoms (only C and H atoms) which > includes neatly 16 methyl groups as substitutions in G03w, and the method > is b3lyp/3-21g*. During the optimization the Maximum Force > and RMS Forces are sometimes converging, Maximum > Displacement and RMS     Displacements are not converging and the > molecules energy is oscillating. I am using following keywords in route > section as > > %mem=1500mb > %nproc=4 > #p opt=(gdiis,maxcycle=200) b3lyp/3-21g* scf=maxcycle=500 > > Please give me suggestion > > Thanks in advance > > Joshi > > > > Add more friends to your messenger and enjoy! Go to > http://messenger.yahoo.com/invite/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Mon Nov 3 06:25:01 2008 From: "sudipta sinha sudipta.mml^gmail.com" To: CCL Subject: CCL: geometric definition of major and minor groove Message-Id: <-38010-081103062159-20380-R0uJMP4+b0vJ5UAmDkAhgw^-^server.ccl.net> X-Original-From: "sudipta sinha" Content-Type: multipart/alternative; boundary="----=_Part_30340_7841784.1225711308941" Date: Mon, 3 Nov 2008 16:51:48 +0530 MIME-Version: 1.0 Sent to CCL by: "sudipta sinha" [sudipta.mml-#-gmail.com] ------=_Part_30340_7841784.1225711308941 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear users, I want know the geometric definition (or algorithm) of the spaces filled by major and minor groove of a DNA. I know those base pairs by which major and minor grooves are forming. Using this little information, is it possible to solve my problem. If anybody aware about this problem, please let me know. It is very useful to me. I am waiting for your early reply. Thanks in advance Sudipta ------=_Part_30340_7841784.1225711308941 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear users,
              
                 I want know the geometric definition (or algorithm) of the spaces filled by major and minor groove of  a DNA.  I know those base pairs by which major  and minor grooves are forming.  Using  this  little information, is it possible to solve my problem. If anybody aware about this problem, please let me know. It is very useful to me. I am waiting for your early reply.

Thanks in advance
Sudipta
------=_Part_30340_7841784.1225711308941-- From owner-chemistry@ccl.net Mon Nov 3 09:13:00 2008 From: "Vihar Georgiev vihgeo=-=chem.gla.ac.uk" To: CCL Subject: CCL: DLPOLY Message-Id: <-38011-081031090056-32364-WlpKDLEnrUOcdNqQaJA3sA]=[server.ccl.net> X-Original-From: Vihar Georgiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 31 Oct 2008 12:11:32 +0000 MIME-Version: 1.0 Sent to CCL by: Vihar Georgiev [vihgeo**chem.gla.ac.uk] sabri alkis alkis{}ufl.edu wrote: > Sent to CCL by: "sabri alkis" [alkis(a)ufl.edu] > Dear DLPOLY users, > > We have Co atoms coming inside the organic molecules and we want to fix the z-coordinates of these Co atoms and let the x-y coordinates free to move. Which subroutine should I go to? what should I change in that routine? Which subroutine handles this? We just want to fix the z-coordinates of these atoms in the system. Then calculate the force on these atoms then integrate the force with respect to z value to get the free energy. > > > Thanks, for your help. > > > Sabri...> > > > Hello Sabri, I really would like to help you but you need to give me more information. What are you want to do exactly- Quantum mechanic calculation, MM and MD or what is your main idea? I am doing more quantim chemistry staff, I am not so familiar with MD like you probably so we can share opinion or information. Accourding to me I don't know what you mean only to fix only z-coordinates but I thing that you can fix the position of the atoms in the space and this include x,y,z coordinates. If you move x and y you will move z as well. So I thing that you need to fix the Co atoms coordinates and make geometry optimization of the other organic part. I don't know if this is the answer that you looking for but this is that I have in my head for now. If you give me more information we can discuss more. So see you soon :)) From owner-chemistry@ccl.net Mon Nov 3 09:48:01 2008 From: "Christina Grindon chris . ccpb.ac.uk" To: CCL Subject: CCL: Conference announement Message-Id: <-38012-081103083523-19334-7lXsYbiiytIt9iVxJYPwiQ**server.ccl.net> X-Original-From: "Christina Grindon" Date: Mon, 3 Nov 2008 08:35:19 -0500 Sent to CCL by: "Christina Grindon" [chris . ccpb.ac.uk] Biomolecular Simulation 2009 CCPB will be holding their annual conference in York from 6th - 8th January 2009. The conference will be held at the Yorkshire Museum & Gardens in the city centre close to many of York's historical sites. The invited speakers are confirmed as: Nathan Baker (Washington University in St Louis, US) Paolo Carloni (SISSA, Italy) Peter Tieleman (University of Calgary, Canada) Jed Pitera (IBM Research, US) Andrew Leach (GlaxoSmithKline, UK) Bojan Zagrovic (Mediterranean Institute for Life Sciences, Croatia) Richard Lavery (Intitut de Biologie et Chimie des Protines, France) We are also accepting abstracts for oral and poster presentations, with the deadline of 14 November 2008. Early bird registration is open until 14 November 2008, with the final registration deadline of 28 November 2008. For further information about the conference, visit the conference website at: www.ccpb.ac.uk/events/conference/2009/ We look forward to seeing you in York in the new year! -- Dr Christina Grindon Community Development Officer CCPB Web: http://www.ccpb.ac.uk Email: chris*ccpb.ac.uk From owner-chemistry@ccl.net Mon Nov 3 10:22:00 2008 From: "Marcel Swart marcel.swart|*|icrea.es" To: CCL Subject: CCL:G: mail from Joshi Message-Id: <-38013-081103085459-20375-6iwh+f173ZkDPSgDAFHvvQ.:.server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-3-450450296 Date: Mon, 3 Nov 2008 14:17:49 +0100 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Marcel Swart [marcel.swart**icrea.es] --Apple-Mail-3-450450296 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Note also the following paper, for hydrocarbons it gives good and =20 fast results (seconds on regular PC): http://dx.doi.org/10.1021/ct8003222 Thermochemistry of Hydrocarbons. Back to Extended H=FCckel Theory On Nov 3, 2008, at 10:41 AM, Kalju Kahn kalju]=3D[chem.ucsb.edu wrote: > > Sent to CCL by: "Kalju Kahn" [kalju:+:chem.ucsb.edu] > Joshi, > > Are you sure that you need B3LYP/3-21G* geometry for this structure? > Seems like molecular mechanics with MM3 might be better suited for > optimizing a large hydrocarbon. > > If you need DFT geometry for some reason, try to freeze all =20 > dihedrals and > optimize bond distances and angles first. Small deviations of =20 > torsional > angles around single bonds is more acceptable than an unusually =20 > stretched > bond for calculation of some molecular properties. > > Kalju > >> Dear CCLers; Hi >> >> I am optimizing a molecule having 387 atoms (only C and H atoms) =20 >> which >> includes neatly 16 methyl groups as substitutions in G03w, and the =20= >> method >> is b3lyp/3-21g*. During the optimization the Maximum Force >> and=C2 RMS=C2 Forces are sometimes converging,=C2 Maximum >> Displacement=C2 and=C2 RMS=C2 =C2 =C2 =C2 Displacements are not = converging =20 >> and the >> molecules energy is oscillating. I am using=C2 following keywords in =20= >> route >> section as >> >> %mem=3D1500mb >> %nproc=3D4 >> #p opt=3D(gdiis,maxcycle=3D200) b3lyp/3-21g* scf=3Dmaxcycle=3D500 >> >> Please give me suggestion >> >> Thanks in advance >> >> Joshi >> >> >> >> Add more friends to your messenger and enjoy! Go to >> http://messenger.yahoo.com/invite/ > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kalju Kahn > Department of Chemistry and Biochemistry > UC Santa Barbara, CA 93106 > > > > -=3D This is automatically added to each message by the mailing =20 > script =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: =20 > search)> > =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 dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart:+:icrea.es marcel.swart:+:udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =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 --Apple-Mail-3-450450296 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Note also the following paper, for hydrocarbons it gives good and fast = results (seconds on regular = PC):

http://dx.doi.org/10.1021/ct8003222

=
Thermochemistry of = Hydrocarbons. Back to Extended H=FCckel Theory

On Nov 3, 2008, at 10:41 = AM, Kalju Kahn kalju]=3D[chem.ucsb.edu wrote:


Sent to = CCL by: "Kalju Kahn" [kalju:+:chem.ucsb.edu]
Joshi,

Are you sure that you need = B3LYP/3-21G* geometry for this structure?=A0
Seems = like molecular mechanics with MM3 might be better suited for
optimizing a large hydrocarbon.

If you = need DFT geometry for some reason, try to freeze all dihedrals = and
optimize bond distances and = angles first.=A0 Small = deviations of torsional
angles around = single bonds is more acceptable than an unusually stretched
bond for calculation of some molecular = properties.

Kalju

Dear = CCLers; Hi

I am optimizing a molecule having 387 atoms (only C = and H atoms) which
includes neatly 16 methyl = groups as substitutions in G03w, and the method
is b3lyp/3-21g*. During the optimization the Maximum = Force
and=C2=A0RMS=C2=A0Forces are = sometimes converging,=C2=A0Maximum
molecules = energy is oscillating. I am using=C2=A0following keywords in = route
section as

%nproc=3D4
#p opt=3D(gdiis,maxcycle=3D200) b3lyp/3-21g* = scf=3Dmaxcycle=3D500
Please give me = suggestion

Thanks in advance




=A0 =A0 =A0 Add more friends to = your messenger and enjoy! Go to

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of = Chemistry and Biochemistry
UC Santa = Barbara, CA 93106



-=3D This is = automatically added to each message by the mailing script =3D-
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
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E-mail to administrators: CHEMISTRY-REQUEST:+:ccl.net = or use

Subscribe/Unsubscribe:=A0

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http:/= /server.ccl.net/chemistry/announcements/conferences/

Search = Messages: http://www.ccl.net/htdig=A0 (login: ccl, Password: = search)

If your mail bounces from CCL with 5.7.1 error, = check:




dr. Marcel = Swart

ICREA = researcher=A0at
Institut de Qu=EDmica = Computacional
Universitat de = Girona

Parc Cient=EDfic i = Tecnol=F2gic
Edifici Jaume Casademont (despatx = A-27)
17003 Girona
Catalunya = (Spain)

tel
marcel.swart:+:udg.edu



=

= --Apple-Mail-3-450450296-- From owner-chemistry@ccl.net Mon Nov 3 11:45:00 2008 From: "Jonathan E Stevens stevenje**udmercy.edu" To: CCL Subject: CCL:G: available user interfaces for g03 Message-Id: <-38014-081103114158-11483-DDGKrZwksgNOQaCjLQ6O6w^server.ccl.net> X-Original-From: "Jonathan E Stevens" Date: Mon, 3 Nov 2008 11:41:55 -0500 Sent to CCL by: "Jonathan E Stevens" [stevenje.:.udmercy.edu] Hello, I am interested in free or inexpensive user interfaces for Gaussian 03. In the past I have worked with the Molecule (for mac) program which historically has had a low-cost site license, and I have recently downloaded and installed the free Arguslab 4.0 package. Does anyone know of similar software? Thanks. From owner-chemistry@ccl.net Mon Nov 3 12:52:01 2008 From: "Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= ejjuarez|a|icmab.es" To: CCL Subject: CCL:G: available user interfaces for g03 Message-Id: <-38015-081103123839-13455-jAN2YyW/jwbElE5wp+Bmjg#server.ccl.net> X-Original-From: Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Mon, 03 Nov 2008 18:34:51 +0100 Mime-Version: 1.0 Sent to CCL by: Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= [ejjuarez##icmab.es] Hello, I am using the Gabedit of Abdul-Rahman ALLOUCHE. It is multiplataform and creates inputs for Gaussian03, Mopac... It is capable to send jobs to remote hosts and it can read the output file... http://gabedit.sourceforge.net/ El lun, 03-11-2008 a las 11:41 -0500, Jonathan E Stevens stevenje**udmercy.edu escribió: > Sent to CCL by: "Jonathan E Stevens" [stevenje.:.udmercy.edu] > Hello, > > I am interested in free or inexpensive user interfaces for > Gaussian 03. In the past I have worked with the Molecule (for mac) program > which historically has had a low-cost site license, and I have recently downloaded and installed the free Arguslab 4.0 package. Does anyone know of similar software? > > Thanks.> ________________________________________________________________________ Emilio José Juárez-Pérez PhD Student ICMAB-CSIC Campus UAB 08193 Bellaterra (Barcelona) Spain. ejjuarez!=!icmab.es http://www.emiliojuarez.es Tel. + 34 93 580 1853 (ext. 255) Fax + 34 93 580 5729 ________________________________________________________________________ From owner-chemistry@ccl.net Mon Nov 3 13:27:00 2008 From: "Dr Ponnadurai Ramasami ramchemi[]intnet.mu" To: CCL Subject: CCL: 4th Workshop on Computational Chemistry and Its Applications (Part of ICCS 2009)/ REMINDER Message-Id: <-38016-081103115445-17911-FEyjc+/TggjDV3qDFEtT0Q:server.ccl.net> X-Original-From: "Dr Ponnadurai Ramasami" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0098_01C93DF6.ABDA9D50" Date: Mon, 3 Nov 2008 20:56:41 +0400 MIME-Version: 1.0 Sent to CCL by: "Dr Ponnadurai Ramasami" [ramchemi[A]intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_0098_01C93DF6.ABDA9D50 Content-Type: text/plain; charset="windows-1256" Content-Transfer-Encoding: quoted-printable Sorry if you receive multiple copies Kindly foward to those who may be interested Let me know if you need more details. Ramasami DEADLINE FOR FULL PAPER IS 6TH DECEMBER 2008 -------------------------------------------------------------------------= ------- THIS IS AN INVITATION TO SUBMIT PAPERS TO BE CONSIDERED FOR THE 4TH = WORKSHOP ON COMPUTATIONAL CHEMISTRY AND ITS APPLICATIONS (PART OF ICCS = 2009) ICCS 2009 will be held from 25th to 27th May 2009 at Baton Rouge, = Louisiana, U.S.A.=20 Website: http://www.iccs-meeting.org/ Topics for the workshop will include aspects of computational chemistry = such as (but are not limited to): (i) Methods: Semiempirical, force fields, ab initio, density = functional=20 (ii) Applications: Kinetics, reaction mechanisms, catalysis, molecular = properties, conformational analysis, thermodynamics (iii) Research involving computational chemistry (iv) Computational chemistry in chemistry education (iv) Interdisciplinary computational research involving chemistry is = specially invited Papers (maximum 8 pages) should be prepared according to the rules of = LNCS (Lecture Notes in Computer Science, = http://www.springer.com/computer/lncs?SGWID=3D0-164-7-72376-0#anchor1) Papers should be submitted in pdf or word file format.=20 Paper submissions should be done electronically, using submission system = on page: http://www.iccs-meeting.org/iccs2009/papers/upload.php All papers will be reviewed by three independent reviewers and IF = ACCEPTED WILL BE PUBLISHED IN LNCS. DEADLINE FOR FULL PAPER IS 6TH DECEMBER 2008 Website for the workshop is = http://www.uom.ac.mu/Faculties/FOS/Chemistry/cca/ Workshop Organisers are=20 Dr Ponnadurai Ramasami and Prof Henry Schaefer III ------=_NextPart_000_0098_01C93DF6.ABDA9D50 Content-Type: text/html; charset="windows-1256" Content-Transfer-Encoding: quoted-printable
Sorry if = you receive=20 multiple copies
Kindly = foward to those=20 who may be interested
Let me know = if you need=20 more details.
Ramasami
DEADLINE FOR FULL PAPER IS = 6TH DECEMBER=20 2008
THIS IS AN=20 INVITATION TO SUBMIT PAPERS TO BE CONSIDERED FOR THE 4TH WORKSHOP ON=20 COMPUTATIONAL CHEMISTRY AND ITS APPLICATIONS (PART OF ICCS=20 2009)
 
ICCS 2009 will be held from = 25th to 27th May 2009 at Baton Rouge, Louisiana, U.S.A. =
Website: http://www.iccs-meeting.org/
 
Topics for the workshop = will include=20 aspects of computational chemistry such as (but are not limited=20 to):
(i)   Methods:  Semiempirical, force fields, = ab=20 initio, density functional
(ii) Applications: Kinetics, = reaction=20 mechanisms, catalysis, molecular properties, conformational analysis,=20 thermodynamics
(iii) Research involving computational = chemistry
(iv)=20 Computational chemistry in chemistry education
(iv) Interdisciplinary = computational research involving chemistry is specially = invited
 
Papers (maximum 8 pages) = should be=20 prepared according to the rules of LNCS (Lecture=20 Notes in Computer Science, http://www.springer.com/computer/lncs?SGWID=3D0-164-7-72376-0#an= chor1)
Papers should be = submitted in=20 pdf or = word=20 file format.
Paper submissions should be done=20 electronically, using submission = system on=20 page:
http://ww= w.iccs-meeting.org/iccs2009/papers/upload.php
All papers will be reviewed by three independent = reviewers and IF=20 ACCEPTED WILL BE PUBLISHED IN LNCS.
 
DEADLINE FOR FULL=20 PAPER IS 6TH DECEMBER 2008
 
Website for = the workshop is=20 http://www.uom.ac.mu/Faculties/FOS/Chemistry/cca/
Workshop Organisers are =
Dr Ponnadurai = Ramasami and=20 Prof Henry Schaefer III
------=_NextPart_000_0098_01C93DF6.ABDA9D50-- From owner-chemistry@ccl.net Mon Nov 3 14:07:01 2008 From: "chongwen zhou cwzhou2008*gmail.com" To: CCL Subject: CCL: Converge faliure in molpro Message-Id: <-38017-081103133406-16399-WmEaavXOd17XOV31rUtqMw]_[server.ccl.net> X-Original-From: "chongwen zhou" Date: Mon, 3 Nov 2008 13:34:01 -0500 Sent to CCL by: "chongwen zhou" [cwzhou2008^gmail.com] Dear all, I have used the molpro to calculate the single point energy. But it alway error terminated because of the converge failure. like the following: Molecular orbital dump at record 2100.2 ITERATION DDIFF GRAD ENERGY 2-EL.EN. DIPOLE MOMENTS DIIS 1 0.000D+00 0.000D+00 -385.02831695 2230.036254 60.203182 -8.048619 0.000000 0 ........ ........ 40 0.142D-01 0.114D-02 -531.37600942 1618.657978 -4.578162 -4.197611 0.000000 9 ?APPARENTLY NO CONVERGENCE, EXIT AFTER THREE FURTHER ITERATIONS 41 0.219D-01 0.111D-02 -531.37945850 1618.510077 -4.346976 -4.332696 0.000000 9 ........ ........ ITER. NORM CORR.ENERGY TOTAL ENERGY ENERGY CHANGE DEN1 VAR(S) VAR(P) DIIS TIME 1 139.11293892 -1.75996564 -533.17759857 -1.75996564 -0.35035335 0.72D+00 0.12D+03 0 0 3120.91 UNREASONABLE NORM. CALCULATION STOPPED Can you tell me how can i overcome this problem? Thank you so much! From owner-chemistry@ccl.net Mon Nov 3 14:36:00 2008 From: "Massimiliano Arca marca/./unica.it" To: CCL Subject: CCL: available user interfaces for g03 Message-Id: <-38018-081103125919-23323-3G6L2CnMl2KjM0DLj2Qb8A : server.ccl.net> X-Original-From: "Massimiliano Arca" Date: Mon, 3 Nov 2008 12:59:15 -0500 Sent to CCL by: "Massimiliano Arca" [marca^^^unica.it] You probably need something such as GaussView, which anyhow is commercial (and expensive). If your needs are not too complex, you could try Molden or Gabedit. From owner-chemistry@ccl.net Mon Nov 3 15:19:00 2008 From: "errol lewars elewars%x%trentu.ca" To: CCL Subject: CCL:G: mail from Joshi Message-Id: <-38019-081103100933-21427-+By6ob9BbJYxn/Nh0GW5qw_-_server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 03 Nov 2008 09:08:05 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars^^^trentu.ca] 2008 Nov 03 Are you starting from a good input geometry and using a good Hessian (I assume you are using the Berny algorithm)? A molecular mechanics geometry and Hessian, or an AM1 or PM3 geometry and Hessian, may help. E. Lewars ===== laxmikanth rao lkjoshiji,yahoo.com wrote: > Dear CCLers; Hi > > I am optimizing a molecule having 387 atoms (only C and H atoms) which > includes neatly 16 methyl groups as substitutions in G03w, and the > method is b3lyp/3-21g*. During the optimization the Maximum Force > and RMS Forces are sometimes converging, Maximum > Displacement and RMS Displacements are not converging and the > molecules energy is oscillating. I am using following keywords in > route section as > > %mem=1500mb > %nproc=4 > #p opt=(gdiis,maxcycle=200) b3lyp/3-21g* scf=maxcycle=500 > > Please give me suggestion > > Thanks in advance > > Joshi > > > ------------------------------------------------------------------------ > Add more friends to your messenger and enjoy! Invite them now. > From owner-chemistry@ccl.net Mon Nov 3 16:14:00 2008 From: "John McKelvey jmmckel . gmail.com" To: CCL Subject: CCL:G: mail from Joshi Message-Id: <-38020-081103153637-28972-htAEnkSeTC6LrSGHsG67Mw{=}server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_90978_2210072.1225744577206" Date: Mon, 3 Nov 2008 15:36:17 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel+*+gmail.com] ------=_Part_90978_2210072.1225744577206 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Perhaps things have changed, and I've forgotten that, but I know that STO-NG* basis sets put d orbitals on the Na-Cl row of the periodic table, and I thought the same was true for 3-21G*.. Am I incorrect? Also, why not try PM6/MOPAC2007 for this for a starting pass at the geometry, along with AIGOUT which prepares a GXY input geometry Z-Matrix? Cheers! John McKelvey On Mon, Nov 3, 2008 at 8:17 AM, Marcel Swart marcel.swart|*|icrea.es < owner-chemistry%x%ccl.net> wrote: > Note also the following paper, for hydrocarbons it gives good and fast > results (seconds on regular PC): > http://dx.doi.org/10.1021/ct8003222 > > *Thermochemistry of Hydrocarbons. Back to Extended H=FCckel Theory* > * > * > On Nov 3, 2008, at 10:41 AM, Kalju Kahn kalju]=3D[chem.ucsb.edu wrote: > > > Sent to CCL by: "Kalju Kahn" [kalju:+:chem.ucsb.edu] > Joshi, > > Are you sure that you need B3LYP/3-21G* geometry for this structure? > Seems like molecular mechanics with MM3 might be better suited for > optimizing a large hydrocarbon. > > If you need DFT geometry for some reason, try to freeze all dihedrals and > optimize bond distances and angles first. Small deviations of torsional > angles around single bonds is more acceptable than an unusually stretched > bond for calculation of some molecular properties. > > Kalju > > Dear CCLers; Hi > > I am optimizing a molecule having 387 atoms (only C and H atoms) which > includes neatly 16 methyl groups as substitutions in G03w, and the method > is b3lyp/3-21g*. During the optimization the Maximum Force > and=C2 RMS=C2 Forces are sometimes converging,=C2 Maximum > Displacement=C2 and=C2 RMS=C2 =C2 =C2 =C2 Displacements are not convergi= ng and the > molecules energy is oscillating. I am using=C2 following keywords in rout= e > section as > > %mem=3D1500mb > %nproc=3D4 > #p opt=3D(gdiis,maxcycle=3D200) b3lyp/3-21g* scf=3Dmaxcycle=3D500 > > Please give me suggestion > > Thanks in advance > > Joshi > > > > Add more friends to your messenger and enjoy! Go to > http://messenger.yahoo.com/invite/ > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kalju Kahn > Department of Chemistry and Biochemistry > UC Santa Barbara, CA 93106 > > > > -=3D This is automatically added to each message by the mailing script = =3D-> the strange characters on the top line to the %x% sign. You can also> > E-mail to subscribers: CHEMISTRY%x%ccl.net or use= :> > E-mail to administrators: CHEMISTRY-REQUEST%x%ccl.netor use> > > > =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 > dr. Marcel Swart > > ICREA researcher at > Institut de Qu=EDmica Computacional > Universitat de Girona > > Parc Cient=EDfic i Tecnol=F2gic > Edifici Jaume Casademont (despatx A-27) > Pic de Peguera 15 > 17003 Girona > Catalunya (Spain) > > tel > +34-972-183240 > fax > +34-972-183241 > e-mail > marcel.swart%x%icrea.es > marcel.swart%x%udg.edu > web > http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 > http://iqc.udg.edu/~marcel > =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 > > > > > ------=_Part_90978_2210072.1225744577206 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Perhaps things have changed, and I've forgotten that, but I know that S= TO-NG* basis sets put d orbitals on the Na-Cl row of the periodic table, an= d I thought the same was true for 3-21G*.. Am I incorrect?

Also,&nbs= p; why not try PM6/MOPAC2007 for this for a starting pass at the geometry, = along with AIGOUT which prepares a GXY input geometry Z-Matrix?

Cheers!

John McKelvey

On Mon, = Nov 3, 2008 at 8:17 AM, Marcel Swart marcel.swart|*|icrea.es <owner-chemistry%x%ccl.net> wrote:
Note also the following paper, for hydrocarbons it gives good and fast resu= lts (seconds on regular PC):




chem.ucsb.edu]
Joshi,

Are you sure that you need= B3LYP/3-21G* geometry for this structure? 
Seems like molecular mechanics with MM3 might be better suited for
optimizing a large hydrocarbon.

If y= ou need DFT geometry for some reason, try to freeze all dihedrals and
optimize bond distances and angles first.=   Small deviations of torsional
bond for calculation of some molecular properti= es.

Kalju
=
Dear CCLers; Hi

I am optimizing a molecule havi= ng 387 atoms (only C and H atoms) which
includes neatly 16 methyl groups as substitutio= ns in G03w, and the method
is b3lyp/3-21g*= . During the optimization the Maximum Force
and=C2 RMS=C2 Forces are sometimes converging,=C2 Maximum
Displacement=C2 and=C2 RMS=C2 = ;=C2 =C2 =C2  Displacements are not converging and the
=
molecules energy is oscillating. I am using=C2&= nbsp;following keywords in route
section as

= %mem=3D1500mb
%nproc=3D4
#p opt=3D(gdiis,maxcycle=3D200) b3lyp/3-21g* scf=3Dmaxcycle=3D500

Please give me suggestion

Thanks in advance

Joshi



      Add more friends to yo= ur messenger and enjoy! Go to


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and= Biochemistry
UC Santa Barbara, CA 93106



-=3D This is automatically added to each message by the = mailing script =3D-
To recover the email a= ddress of the author of the message, please change
the strange characters on the top line to= the %x% sign. You can also

E-mail to subscribers: CHEMISTRY%x%ccl.net= or use:



------=_Part_90978_2210072.1225744577206-- From owner-chemistry@ccl.net Mon Nov 3 21:37:01 2008 From: "Vlad vvv900{=}anusf.anu.edu.au" To: CCL Subject: CCL:G: available user interfaces for g03 Message-Id: <-38021-081103172915-4895-EtCAPjz+f9WC7hfUeBdJ7w^server.ccl.net> X-Original-From: Vlad Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1251; format=flowed Date: Tue, 04 Nov 2008 09:28:55 +1100 MIME-Version: 1.0 Sent to CCL by: Vlad [vvv900[a]anusf.anu.edu.au] Hi Jonathan, > I am interested in free or inexpensive user interfaces for > Gaussian 03. In the past I have worked with the Molecule (for mac) program > which historically has had a low-cost site license, and I have recently downloaded and installed the free Arguslab 4.0 package. Does anyone know of similar software? Jamberoo (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html ) can parse and visualize G03 input and output files. In the case of output files, it can animate optimization pathway using interactive charting, animate vibrations, and show displacement vectors. Also, it can show molecular orbitals, electrostatic potential, etc. from g03 cube file. Best wishes, Vlad -- Dr Vladislav Vassiliev Computational Chemist ANU Supercomputer Facility, 56 Leonard Huxley Building, The Australian National University, Canberra ACT 0200 Australia Telephone : +61 2 6125 9694 Fax : +61 2 6125 8199 WWW : http://sf.anu.edu.au/~vvv900/