From owner-chemistry@ccl.net Thu Sep 25 04:07:02 2008 From: "Simmie, John john.simmie#%#nuigalway.ie" To: CCL Subject: CCL: Referencing chemical equations in LaTeX Message-Id: <-37802-080925035220-26218-+NLNov7xMQRw+RrYm/TwKA_-_server.ccl.net> X-Original-From: "Simmie, John" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C91EDF.02E51B4E" Date: Thu, 25 Sep 2008 08:16:54 +0100 MIME-Version: 1.0 Sent to CCL by: "Simmie, John" [john.simmie=-=nuigalway.ie] This is a multi-part message in MIME format. ------_=_NextPart_001_01C91EDF.02E51B4E Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable I presume that you are using the book/report class ? If so put this in the preamble \renewcommand{\theequation}{\arabic{equation}} Incidentally \eqref{rxn1} from Amsmath automatically gives you the () and is a neater way to cross-reference If you are using the article class then the automatic numbering is as you requested so no changes are needed at all I prefer to use AmsMath's align environment for multiple reactions and to use \mathrm{} which sets reaction in a proper upright font, and aligns both your examples on the =3D in this case You must have \usepackage{amsmath} in your preamble of course=20 \begin{align} \mathrm{C_9H_7 + O_2} & =3D \mathrm{C_6H_{5O} + C_3H_{2O}} \label{C9H7O21}\\ \mathrm{C_9H_7 + O_2} & =3D \mathrm{C_7H_7 + CO + CO} = \label{C9H7O22} \end{align} You can flushleft in addition but I don't think that this looks well to chemists .. For single examples just use the \begin{equation} environment viz \begin{equation} \mathrm{C_9H_7 + O_2 =3D C_6H_{5O} + C_3H_2O} \label{C9H7O21} \end{equation} Finally, if you want to have separate counters for ordinary equations and chemical reactions then you have to define a new environment (\chemeq ?) and a new counter ... but that's another story Emeritus Professor John Simmie::Combustion Chemistry Centre::National University of Ireland, Galway work:+353-91-492451, home:+353-91-592462::mobile:+353-87-805-9948 john.simmie+*+nuigalway.ie ------_=_NextPart_001_01C91EDF.02E51B4E Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Re: Referencing chemical equations in LaTeX

I presume that = you are using the book/report class ?

If so put this = in the preamble

\renewcommand{\theequation}{\arabic{equation}}

Incidentally = \eqref{rxn1} from Amsmath automatically gives you the = () and is a = neater way to cross-reference

If you are using the = article class then the automatic numbering is as you = requested so = no changes are needed at all

I prefer to use AmsMath’s align environment for multiple = reactions and = to use \mathrm{}

which sets = reaction in a proper upright font, and aligns both your examples on = the =3D in = this case

You must have = \usepackage{amsmath} in your preamble of course

\begin{align}

\mathrm{C_9H_7 = + O_2} & =3D \mathrm{C_6H_{5O} + C_3H_{2O}} \label{C9H7O21}\\

\mathrm{C_9H_7 = + O_2} & =3D \mathrm{C_7H_7 + CO + CO}      \label{C9H7O22}  =

\end{align}

You can = flushleft in addition but I don't think that this looks well to chemists = ..

For single = examples = just use the \begin{equation} environment viz

\begin{equation}

\mathrm{C_9H_7 + O_2 =3D C_6H_{5O} + C_3H_2O} = \label{C9H7O21}

\end{equation}

Finally, if you = want to have separate counters for ordinary equations and chemical = reactions then you have to

define a new = environment (\chemeq ?) and a new counter … but that’s another story

Emeritus Professor = John Simmie::Combustion Chemistry Centre::National University of = Ireland, Galway

work:+353-91-492451, = home:+353-91-592462::mobile:+353-87-805-9948

john.simmie+*+nuigalway.ie

------_=_NextPart_001_01C91EDF.02E51B4E-- From owner-chemistry@ccl.net Thu Sep 25 05:38:00 2008 From: "Dr Ponnadurai Ramasami ramchemi,+,intnet.mu" To: CCL Subject: CCL: 4th Workshop on Computational Chemistry and Its Applications (Part of ICCS 2009) Message-Id: <-37803-080924234534-30319-6WziWYjpjAt+wlQwOjnxgQ^server.ccl.net> X-Original-From: "Dr Ponnadurai Ramasami" Content-Type: multipart/alternative; boundary="----=_NextPart_000_002E_01C91EDA.10439C60" Date: Thu, 25 Sep 2008 06:43:48 +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_002E_01C91EDA.10439C60 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 -------------------------------------------------------------------------= ------- 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_002E_01C91EDA.10439C60 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
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_002E_01C91EDA.10439C60-- From owner-chemistry@ccl.net Thu Sep 25 09:15:00 2008 From: "mi yang miyang3790^^gmail.com" To: CCL Subject: CCL: PCM vs Onsager Message-Id: <-37804-080925091300-7064-QD1Yd4yUu67JmcAp0LkI7A+/-server.ccl.net> X-Original-From: "mi yang" Date: Thu, 25 Sep 2008 09:12:56 -0400 Sent to CCL by: "mi yang" [miyang3790*|*gmail.com] Hi CCL users I have two questions First Is Onsager method has any advantage over PCM especially in superamolecular optimizations,I mean to say is it still valid..? Secondly I have optimized a complex containing N-H---F ion. The gas phase, at BSSE corrected surface, with Onsager and also in experiment the process is deprotonation and all the structures show considerable increase in the N-H distance (0.8A) at optimized structure but when I used PCM or CPCM taking H as explicit from heavy atom (with pauling or Bondi radii), the optimized structure did not show any significant effect on N-H distance that is against the experiment results and above stated three methods. Is there any need to modify the solvent cavity in CPCM or PCM so that it would show some effect on N-H distance during N-H---F ion optimization like Onsager or others? Or any other solvation method that could correlate with experiment ? I am also wandering due to dealing H as explicit may be erroness in result? Thanks in advance if some one help me out in this conditions. Miyang Northeast normal university china miyang3790.+/-.gmail.com From owner-chemistry@ccl.net Thu Sep 25 09:49:00 2008 From: "Ron Elber ron]~[ices.utexas.edu" To: CCL Subject: CCL: MOIL11 - a new release of the free software MOIL for simulations of molecular mechanics and dynamics Message-Id: <-37805-080925010622-5968-/7FbA/XPK+YXQN80/Q18LA- -server.ccl.net> X-Original-From: Ron Elber Content-Type: multipart/alternative; boundary=Apple-Mail-9--804478445 Date: Wed, 24 Sep 2008 23:10:57 -0500 Mime-Version: 1.0 (Apple Message framework v926) Sent to CCL by: Ron Elber [ron#ices.utexas.edu] --Apple-Mail-9--804478445 Content-Type: text/plain; charset=WINDOWS-1252; format=flowed; delsp=yes Content-Transfer-Encoding: quoted-printable We announce the release of a new version of the package for molecular =20= dynamics and modeling MOIL1 - MOIL11. The complete source code is =20 included. Ready execution files are available for Windows XP, Mac OS/=20 X, and Linux (Fedora). The code is in the public domain. You may use =20 it or any portion of it in any way you like. The only requirement is =20 that references will be made to the original authors in any study that =20= uses MOIL. New codes that build on MOIL should detail the extent of =20 use and include in their release notes the first paragraph of this =20 message. Moil supports the usual set of tools for molecular modeling by =20 classical mechanics, including energy calculations, energy =20 minimization, molecular dynamics, and more. Code is available to =20 simulate curve crossing within the Landau Zener model. Moil allows for =20= reasonably straightforward conversion of PDB files to computable =20 datasets (coordinate and energy templates). Besides =93standard=94 applications MOIL evolves around the research in =20= Ron Elber=92s laboratory. Examples are the Locally Enhanced Sampling =20 Approach2 and reaction path and long time dynamics algorithms 3 that =20 are based on action optimization. Also included the recently developed =20= Milestoning approach for the calculation of kinetics and =20 thermodynamics along a reaction coordinate4. The integration of a =20 coarse-grained model into moil is yet another new feature of MOIL11. Numerous examples and templates are included in the moil/moil.test =20 directory. Documentations are in moil/moil.doc. A dictionary of =20 keywords used in moil is available at moil/moil.doc/dictionary.txt Significant new enhancements to the older version(s) include Get a pre built code http://clsb.ices.utexas.edu/prebuilt or signed on =20= a SVN server for continuous updates of source code = https://wiki.ices.utexas.edu/clsb/wiki A new visualization program (zmoil) for graphic display of individual =20= structures, dynamics, reaction paths and overlay of multiple =20 structures, read PDB CRD DCD and (MOIL specific) PTH formatted files. =20= (by Thomas Blom and Baohua Wang) Enhanced graphic interface moil.tcl for numerical simulations with =20 numerous bug fixes. Not all moil modules are supported by the graphic =20= interface (by Thomas Blom and Baohua Wang) A new coarse-grained model of proteins (two points per amino acid) for =20= energy, minimization, dynamics and path calculations (by Peter Majek) Replica exchange (by Serdal Kirmizialtin) New code for stochastic optimization of approximate trajectories with =20= large step (SDEL by Peter Majek) Steepest descent path calculation by action optimization (sdp module =20 by Ron Elber and Peter Majek) Milestoning simulations of kinetics (the fp module by Anthony West) Implementation of OPLS DNA/RNA force field in addition to OPLS for =20 proteins and liquid simulations (by Serdal Kirmizialtin) Calculation of pressure (by Luca Maragliano) MOIL11 team: Thomas Blom, Peter Majek, Serdal Kirmizialtin, and Ron =20 Elber A few references 1 R. Elber, A. Roitberg, C. Simmerling et al., Computer =20 Physics Communications 91 (1-3), 159 (1995). 2 C. Simmerling and R. Elber, Journal of the American =20 Chemical Society 116 (6), 2534 (1994); G. Verkhivker, R. Elber, and Q. =20= H. Gibson, Journal of the American Chemical Society 114 (20), 7866 =20 (1992); A. Roitberg and R. Elber, Journal of Chemical Physics 95 (12), =20= 9277 (1991); R. Elber and M. Karplus, Journal of the American Chemical =20= Society 112 (25), 9161 (1990). 3 W. Nowak, R. Czerminski, and R. Elber, Journal of the =20 American Chemical Society 113 (15), 5627 (1991); R. Czerminski and R. =20= Elber, International Journal of Quantum Chemistry, 167 (1990); R. =20 Olender and R. Elber, Theochem-Journal of Molecular Structure 398, 63 =20= (1997); P. Majek, H. Weinstein, and R. Elber, Pathways of =20 conformational transition in proteins. (2007). 4 A. M. A. West, R. Elber, and D. Shalloway, Journal of =20 Chemical Physics 126 (14) (2007). =20= --Apple-Mail-9--804478445 Content-Type: text/html; charset=WINDOWS-1252 Content-Transfer-Encoding: quoted-printable
We announce the release of a new version of the = package for molecular dynamics and modeling MOIL1 -  MOIL11. The complete source = code is included. Ready execution files are available for Windows XP, Mac OS/X, and Linux = (Fedora). The code is in the public domain. You may use it or any portion of it in any = way you like. The only requirement is that references will be made to the = original authors in any study that uses MOIL. New codes that build on MOIL should = detail the extent of use and include in their release notes the first paragraph = of this message.
 
Moil supports the usual set of tools for = molecular modeling by classical mechanics, including energy calculations, energy = minimization, molecular dynamics, and more. Code is available to simulate curve crossing within = the Landau Zener model. Moil allows for reasonably straightforward = conversion of PDB files to computable datasets (coordinate and energy templates). =
 
Besides =93standard=94 applications MOIL = evolves around the research in Ron Elber=92s laboratory. Examples are the Locally Enhanced = Sampling Approach2 and reaction path and long time dynamics algorithms 3 that are based on action optimization. Also included the recently = developed Milestoning approach for the calculation of kinetics and thermodynamics = along a reaction coordinate4. The integration of = a coarse-grained model into moil is yet another new feature of = MOIL11.
 
Numerous examples and templates are included in = the moil/moil.test directory. Documentations are in moil/moil.doc. A = dictionary of keywords used in moil is available at moil/moil.doc/dictionary.txt
 
Significant new enhancements to the older = version(s) include
  1. Get a pre built code http://clsb.ices.utexas.edu/= prebuilt or signed on a SVN server for continuous updates of source code = https://wiki.ices.utexas.edu/clsb/wiki=
  2. A new visualization program (zmoil) for graphic display of individual structures, dynamics, reaction paths and overlay of multiple = structures, read PDB CRD DCD and (MOIL specific) PTH formatted files. (by = Thomas Blom and Baohua Wang)
  3. Enhanced graphic interface moil.tcl for numerical simulations with numerous = bug fixes. Not all moil modules are supported by the graphic = interface  (by Thomas Blom = and Baohua Wang)
  4. A new coarse-grained model of proteins (two points per amino acid) for = energy, minimization, dynamics and path calculations (by Peter Majek)
  5. Replica exchange (by Serdal Kirmizialtin)
  6. New code for stochastic optimization of  approximate trajectories with large step (SDEL by Peter = Majek)
  7. Steepest descent path calculation by action optimization (sdp module by Ron = Elber and Peter Majek)
  8. Milestoning simulations of kinetics (the fp module by Anthony West)
  9. Implementation of OPLS DNA/RNA force field in addition to OPLS for proteins and = liquid simulations (by Serdal Kirmizialtin)
  10. Calculation of pressure (by Luca Maragliano)
 
MOIL11 team: Thomas Blom, Peter Majek, Serdal = Kirmizialtin, and Ron Elber
 
A few references

1        =     R. Elber, A. Roitberg, C. Simmerling et al., Computer Physics = Communications 91 (1-3), 159 = (1995).

2        =     C. Simmerling and R. Elber, Journal of the American Chemical Society = 116 (6), 2534 (1994); G. = Verkhivker, R. Elber, and Q. H. Gibson, Journal of the American Chemical Society = 114 (20), 7866 (1992); = A. Roitberg and R. Elber, Journal of Chemical Physics 95 (12), 9277 (1991); R. Elber and M. Karplus, Journal of the American = Chemical Society 112 (25), 9161 = (1990).

3        =     W. Nowak, R. Czerminski, and R. Elber, Journal of the American Chemical = Society 113 (15), 5627 (1991); = R. Czerminski and R. Elber, International Journal of Quantum Chemistry, 167 (1990); R. Olender and = R. Elber, Theochem-Journal of Molecular Structure 398, 63 (1997); P. Majek, H. Weinstein, and R. = Elber, Pathways of conformational transition in proteins. (2007).

4        =     A. M. A. West, R. Elber, and D. Shalloway, Journal of Chemical Physics = 126 (14) (2007).

 
= --Apple-Mail-9--804478445-- From owner-chemistry@ccl.net Thu Sep 25 17:02:00 2008 From: "Debasis Sengupta dxs-,-cfdrc.com" To: CCL Subject: CCL:G: Gaussian Binary in Intel Xeon and AMD Opteron Message-Id: <-37806-080925165556-9221-9PGASXBTRy3W0blhPcqplA/a\server.ccl.net> X-Original-From: "Debasis Sengupta" Date: Thu, 25 Sep 2008 16:55:53 -0400 Sent to CCL by: "Debasis Sengupta" [dxs ~ cfdrc.com] Hi Everyone, I am planning to buy Linux version of Gaussian 03 binary. I was wondering if the same binary will work for both AMD Opteron as well as Intel Xeon (especially Quadcore). Also, could anybody give me an idea about performance of G03 w.r.t Xeom and Opteron? Thanks in advance. Debasis