This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009) (format=pdflatex 2009.12.22) 24 JAN 2010 14:10 entering extended mode \write18 enabled. %&-line parsing enabled. **markov-model-from-parallel-tempering.tex (./markov-model-from-parallel-tempering.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, german-x-2009-06-19, ngerman-x-2009-06-19, ancientgreek, ibycus, ar abic, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutc h, esperanto, estonian, farsi, finnish, french, galician, german, ngerman, mono greek, greek, hungarian, icelandic, indonesian, interlingua, irish, italian, ku rmanji, latin, latvian, lithuanian, mongolian, mongolian2a, bokmal, nynorsk, po lish, portuguese, romanian, russian, sanskrit, serbian, slovak, slovenian, span ish, swedish, turkish, ukenglish, ukrainian, uppersorbian, welsh, loaded. (/usr/local/texlive/2009/texmf-dist/tex/latex/revtex/revtex4-1.cls Document Class: revtex4-1 2009/10/08:11:23 4.1g (http://publish.aps.org/revtex4 / for documentation) Copyright (c) 2009 The American Physical Society. mailto:revtex@aps.org Licensed under the LPPL: http://www.ctan.org/tex-archive/macros/latex/base/lppl.txt Arthur Ogawa Based on work by David Carlisle . ltxutil [2009/07/07 4.1f]: portions licensed from W. E. Baxter (web at superscr ipt.com) LaTeX Info: Redefining \@centercr on input line 298. Class revtex4-1 Info: Repairing broken LaTeX eqnarray on input line 348. \eqncolsep=\skip41 Class revtex4-1 Info: Repairing hyperref-unfriendly LaTeX definition of \mpfoot note on input line 423. Class revtex4-1 Info: Repairing broken LateX \@sect on input line 754. \intertabularlinepenalty=\count79 \@tbpen=\count80 \@arstrutbox@hline=\box26 Class revtex4-1 Info: Repairing broken LaTeX \@xbitor on input line 1785. Class revtex4-1 Info: Making \typeout \long on input line 1953. ltxfront [2009/10/06/20:20 4.1g]: Arthur Ogawa (after David P. Carlisle) \c@affil=\count81 \c@collab=\count82 \absbox=\box27 ltxgrid [2009/07/07 4.1f]: portions licensed from W. E. Baxter (web at superscr ipt.com) \c@linecount=\count83 \output@latex=\toks14 \box@size@1=\box28 \box@size@2=\box29 \@protection@box=\box30 \@topmark@saved=\toks15 \footins@saved=\box31 \pagesofar=\box32 \footsofar=\box33 \pagegrid@col=\count84 Class revtex4-1 Info: Overriding \@vspace, \@vspacer, \@no@pgbk, \@newline, and \\ on input line 5346. \c@part=\count85 \c@section=\count86 \c@subsection=\count87 \c@subsubsection=\count88 \c@paragraph=\count89 \c@subparagraph=\count90 \abovecaptionskip=\skip42 \belowcaptionskip=\skip43 \c@figure=\count91 \fbox@1=\box34 \c@table=\count92 \fbox@2=\box35 \c@video=\count93 \fbox@4=\box36 \@bibdataout=\write3 \widetext@top=\box37 \widetext@bot=\box38 Class revtex4-1 Info: Selecting society aps on input line 7230. (/usr/local/texlive/2009/texmf-dist/tex/latex/revtex/aps4-1.rtx File: aps4-1 2009/10/08:11:23 4.1g (http://publish.aps.org/revtex4/ for documen tation) Class revtex4-1 Info: RevTeX society APS selected on input line 31. ) Class revtex4-1 Info: Selecting journal prl on input line 7232. Class revtex4-1 Info: APS journal PRL selected on input line 7233. (/usr/local/texlive/2009/texmf-dist/tex/latex/revtex/aps12pt4-1.rtx File: aps12pt4-1 2009/10/08:11:23 4.1g (http://publish.aps.org/revtex4/ for doc umentation) Class revtex4-1 Info: RevTeX pointsize 12pt selected on input line 30. ) (/usr/local/texlive/2009/texmf-dist/tex/latex/textcase/textcase.sty Package: textcase 2004/10/07 v0.07 Text only upper/lower case changing (DPC) ) (/usr/local/texlive/2009/texmf-dist/tex/latex/ltxmisc/url.sty \Urlmuskip=\muskip10 Package: url 2006/04/12 ver 3.3 Verb mode for urls, etc. ) (/usr/local/texlive/2009/texmf-dist/tex/latex/natbib/natbib.sty Package: natbib 2009/07/16 8.31 (PWD, AO) \bibhang=\skip44 \bibsep=\skip45 LaTeX Info: Redefining \cite on input line 694. \c@NAT@ctr=\count94 ) (/usr/local/texlive/2009/texmf-dist/tex/latex/revtex/revsymb4-1.sty Package: revsymb4-1 2009/10/08:11:23 4.1g (http://publish.aps.org/revtex4/ for documentation) LaTeX Info: Redefining \REV@mathfrak on input line 119. )) (/usr/local/texlive/2009/texmf-dist/tex/latex/psnfss/palatino.sty Package: palatino 2005/04/12 PSNFSS-v9.2a (SPQR) ) (/usr/local/texlive/2009/texmf-dist/tex/latex/amsmath/amsmath.sty Package: amsmath 2000/07/18 v2.13 AMS math features \@mathmargin=\skip46 For additional information on amsmath, use the `?' option. (/usr/local/texlive/2009/texmf-dist/tex/latex/amsmath/amstext.sty Package: amstext 2000/06/29 v2.01 (/usr/local/texlive/2009/texmf-dist/tex/latex/amsmath/amsgen.sty File: amsgen.sty 1999/11/30 v2.0 \@emptytoks=\toks16 \ex@=\dimen102 ) LaTeX Info: Redefining \text on input line 53. ) (/usr/local/texlive/2009/texmf-dist/tex/latex/amsmath/amsbsy.sty Package: amsbsy 1999/11/29 v1.2d \pmbraise@=\dimen103 ) (/usr/local/texlive/2009/texmf-dist/tex/latex/amsmath/amsopn.sty Package: amsopn 1999/12/14 v2.01 operator names ) \inf@bad=\count95 LaTeX Info: Redefining \frac on input line 211. \uproot@=\count96 \leftroot@=\count97 LaTeX Info: Redefining \overline on input line 307. \classnum@=\count98 \DOTSCASE@=\count99 LaTeX Info: Redefining \ldots on input line 379. LaTeX Info: Redefining \dots on input line 382. LaTeX Info: Redefining \cdots on input line 467. \Mathstrutbox@=\box39 \strutbox@=\box40 \big@size=\dimen104 LaTeX Font Info: Redeclaring font encoding OML on input line 567. LaTeX Font Info: Redeclaring font encoding OMS on input line 568. \macc@depth=\count100 \c@MaxMatrixCols=\count101 \dotsspace@=\muskip11 \c@parentequation=\count102 \dspbrk@lvl=\count103 \tag@help=\toks17 \row@=\count104 \column@=\count105 \maxfields@=\count106 \andhelp@=\toks18 \eqnshift@=\dimen105 \alignsep@=\dimen106 \tagshift@=\dimen107 \tagwidth@=\dimen108 \totwidth@=\dimen109 \lineht@=\dimen110 \@envbody=\toks19 \multlinegap=\skip47 \multlinetaggap=\skip48 \mathdisplay@stack=\toks20 LaTeX Info: Redefining \[ on input line 2666. LaTeX Info: Redefining \] on input line 2667. ) (/usr/local/texlive/2009/texmf-dist/tex/latex/amsfonts/amssymb.sty Package: amssymb 2009/06/22 v3.00 (/usr/local/texlive/2009/texmf-dist/tex/latex/amsfonts/amsfonts.sty Package: amsfonts 2009/06/22 v3.00 Basic AMSFonts support \symAMSa=\mathgroup4 \symAMSb=\mathgroup5 LaTeX Font Info: Overwriting math alphabet `\mathfrak' in version `bold' (Font) U/euf/m/n --> U/euf/b/n on input line 96. LaTeX Info: Redefining \frak on input line 99. LaTeX Info: Redefining \Bbb on input line 101. )) (/usr/local/texlive/2009/texmf-dist/tex/latex/graphics/graphicx.sty Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR) (/usr/local/texlive/2009/texmf-dist/tex/latex/graphics/keyval.sty Package: keyval 1999/03/16 v1.13 key=value parser (DPC) \KV@toks@=\toks21 ) (/usr/local/texlive/2009/texmf-dist/tex/latex/graphics/graphics.sty Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR) (/usr/local/texlive/2009/texmf-dist/tex/latex/graphics/trig.sty Package: trig 1999/03/16 v1.09 sin cos tan (DPC) ) (/usr/local/texlive/2009/texmf-dist/tex/latex/latexconfig/graphics.cfg File: graphics.cfg 2009/08/28 v1.8 graphics configuration of TeX Live ) Package graphics Info: Driver file: pdftex.def on input line 91. (/usr/local/texlive/2009/texmf-dist/tex/latex/pdftex-def/pdftex.def File: pdftex.def 2009/08/25 v0.04m Graphics/color for pdfTeX \Gread@gobject=\count107 )) \Gin@req@height=\dimen111 \Gin@req@width=\dimen112 ) (/usr/local/texlive/2009/texmf-dist/tex/latex/tools/dcolumn.sty Package: dcolumn 2001/05/28 v1.06 decimal alignment package (DPC) (/usr/local/texlive/2009/texmf-dist/tex/latex/tools/array.sty Package: array 2008/09/09 v2.4c Tabular extension package (FMi) \col@sep=\dimen113 \extrarowheight=\dimen114 \NC@list=\toks22 \extratabsurround=\skip49 \backup@length=\skip50 )) (/usr/local/texlive/2009/texmf-dist/tex/latex/ltxmisc/boxedminipage.sty) (/usr/local/texlive/2009/texmf-dist/tex/latex/tools/verbatim.sty Package: verbatim 2003/08/22 v1.5q LaTeX2e package for verbatim enhancements \every@verbatim=\toks23 \verbatim@line=\toks24 \verbatim@in@stream=\read1 ) (/usr/local/texlive/2009/texmf-dist/tex/latex/hyperref/hyperref.sty Package: hyperref 2009/12/16 v6.79u Hypertext links for LaTeX (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/ifpdf.sty Package: ifpdf 2009/04/10 v2.0 Provides the ifpdf switch (HO) Package ifpdf Info: pdfTeX in pdf mode detected. ) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/ifvtex.sty Package: ifvtex 2008/11/04 v1.4 Switches for detecting VTeX and its modes (HO) Package ifvtex Info: VTeX not detected. ) (/usr/local/texlive/2009/texmf-dist/tex/generic/ifxetex/ifxetex.sty Package: ifxetex 2009/01/23 v0.5 Provides ifxetex conditional ) (/usr/local/texlive/2009/texmf-dist/tex/latex/oberdiek/hycolor.sty Package: hycolor 2009/12/12 v1.6 Color options of hyperref/bookmark (HO) (/usr/local/texlive/2009/texmf-dist/tex/latex/oberdiek/xcolor-patch.sty Package: xcolor-patch 2009/12/12 xcolor patch )) \@linkdim=\dimen115 \Hy@linkcounter=\count108 \Hy@pagecounter=\count109 (/usr/local/texlive/2009/texmf-dist/tex/latex/hyperref/pd1enc.def File: pd1enc.def 2009/12/16 v6.79u Hyperref: PDFDocEncoding definition (HO) ) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty Package: pdftexcmds 2009/12/12 v0.7 Utility functions of pdfTeX for LuaTeX (HO) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/infwarerr.sty Package: infwarerr 2007/09/09 v1.2 Providing info/warning/message (HO) ) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/ifluatex.sty Package: ifluatex 2009/04/17 v1.2 Provides the ifluatex switch (HO) Package ifluatex Info: LuaTeX not detected. ) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/ltxcmds.sty Package: ltxcmds 2009/12/12 v1.1 LaTeX kernel commands for general use (HO) ) Package pdftexcmds Info: LuaTeX not detected. Package pdftexcmds Info: \pdf@primitive is available. Package pdftexcmds Info: \pdf@ifprimitive is available. ) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/etexcmds.sty Package: etexcmds 2007/12/12 v1.2 Prefix for e-TeX command names (HO) Package etexcmds Info: Could not find \expanded. (etexcmds) That can mean that you are not using pdfTeX 1.50 or (etexcmds) that some package has redefined \expanded. (etexcmds) In the latter case, load this package earlier. ) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/intcalc.sty Package: intcalc 2007/09/27 v1.1 Expandable integer calculations (HO) ) (/usr/local/texlive/2009/texmf-dist/tex/latex/latexconfig/hyperref.cfg File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive ) (/usr/local/texlive/2009/texmf-dist/tex/latex/oberdiek/kvoptions.sty Package: kvoptions 2009/12/08 v3.6 Keyval support for LaTeX options (HO) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty Package: kvsetkeys 2009/12/12 v1.6 Key value parser (HO) )) Package hyperref Info: Option `colorlinks' set `true' on input line 2975. Package hyperref Info: Hyper figures OFF on input line 3056. Package hyperref Info: Link nesting OFF on input line 3061. Package hyperref Info: Hyper index ON on input line 3064. Package hyperref Info: Plain pages OFF on input line 3071. Package hyperref Info: Backreferencing OFF on input line 3076. Implicit mode ON; LaTeX internals redefined Package hyperref Info: Bookmarks ON on input line 3272. LaTeX Info: Redefining \href on input line 3490. LaTeX Info: Redefining \url on input line 3509. (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/bitset.sty Package: bitset 2007/09/28 v1.0 Data type bit set (HO) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/bigintcalc.sty Package: bigintcalc 2007/11/11 v1.1 Expandable big integer calculations (HO) )) \Fld@menulength=\count110 \Field@Width=\dimen116 \Fld@charsize=\dimen117 \Field@toks=\toks25 Package hyperref Info: Hyper figures OFF on input line 4469. Package hyperref Info: Link nesting OFF on input line 4474. Package hyperref Info: Hyper index ON on input line 4477. Package hyperref Info: backreferencing OFF on input line 4484. Package hyperref Info: Link coloring ON on input line 4487. Package hyperref Info: Link coloring with OCG OFF on input line 4494. Package hyperref Info: PDF/A mode OFF on input line 4499. (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/atbegshi.sty Package: atbegshi 2009/12/02 v1.10 At begin shipout hook (HO) ) \Hy@abspage=\count111 \c@Item=\count112 \c@Hfootnote=\count113 ) *hyperref using default driver hpdftex* (/usr/local/texlive/2009/texmf-dist/tex/latex/hyperref/hpdftex.def File: hpdftex.def 2009/12/16 v6.79u Hyperref driver for pdfTeX (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/atveryend.sty Package: atveryend 2009/12/11 v1.3 Hooks at very end of document (HO) ) \Fld@listcount=\count114 \c@bookmark@seq@number=\count115 (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/rerunfilecheck.sty Package: rerunfilecheck 2009/12/12 v1.1 Rerun checks for auxiliary files (HO) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/uniquecounter.sty Package: uniquecounter 2009/09/11 v1.0 Provides unlimited unique counter (HO) ) Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 3 26. ) \Hy@SectionHShift=\skip51 ) Class revtex4-1 Info: Patching array package. on input line 77. Class revtex4-1 Info: Robustifying \LaTeX's \boldmath command on input line 77. Class revtex4-1 Info: cite was not loaded (OK!) on input line 77. Class revtex4-1 Info: mcite was not loaded (OK!) on input line 77. Class revtex4-1 Info: multicol was not loaded (OK!) on input line 77. (./markov-model-from-parallel-tempering.aux) \openout1 = `markov-model-from-parallel-tempering.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 77. LaTeX Font Info: ... okay on input line 77. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 77. LaTeX Font Info: ... okay on input line 77. LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 77. LaTeX Font Info: ... okay on input line 77. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 77. LaTeX Font Info: ... okay on input line 77. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 77. LaTeX Font Info: ... okay on input line 77. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 77. LaTeX Font Info: ... okay on input line 77. LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 77. LaTeX Font Info: ... okay on input line 77. LaTeX Font Info: Try loading font information for OT1+ppl on input line 77. (/usr/local/texlive/2009/texmf-dist/tex/latex/psnfss/ot1ppl.fd File: ot1ppl.fd 2001/06/04 font definitions for OT1/ppl. ) (/usr/local/texlive/2009/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] \scratchcounter=\count116 \scratchdimen=\dimen118 \scratchbox=\box41 \nofMPsegments=\count117 \nofMParguments=\count118 \everyMPshowfont=\toks26 \MPscratchCnt=\count119 \MPscratchDim=\dimen119 \MPnumerator=\count120 \everyMPtoPDFconversion=\toks27 ) (/usr/local/texlive/2009/texmf-dist/tex/latex/graphics/color.sty Package: color 2005/11/14 v1.0j Standard LaTeX Color (DPC) (/usr/local/texlive/2009/texmf-dist/tex/latex/latexconfig/color.cfg File: color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive ) Package color Info: Driver file: pdftex.def on input line 130. ) Package hyperref Info: Link coloring ON on input line 77. (/usr/local/texlive/2009/texmf-dist/tex/latex/hyperref/nameref.sty Package: nameref 2009/12/08 v2.34 Cross-referencing by name of section (/usr/local/texlive/2009/texmf-dist/tex/latex/oberdiek/refcount.sty Package: refcount 2008/08/11 v3.1 Data extraction from references (HO) ) (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/gettitlestring.sty Package: gettitlestring 2009/12/13 v1.2 Cleanup title references (HO) ) \c@section@level=\count121 ) LaTeX Info: Redefining \ref on input line 77. LaTeX Info: Redefining \pageref on input line 77. (./markov-model-from-parallel-tempering.out) (./markov-model-from-parallel-tempering.out) \@outlinefile=\write4 \openout4 = `markov-model-from-parallel-tempering.out'. \AtBeginShipoutBox=\box42 Class revtex4-1 Info: Taking \maketitle back from hyperref on input line 77. \openout3 = `markov-model-from-parallel-temperingNotes.bib'. LaTeX Font Info: Font shape `OT1/ppl/bx/n' in size <14.4> not available (Font) Font shape `OT1/ppl/b/n' tried instead on input line 119. LaTeX Font Info: Try loading font information for U+msa on input line 119. (/usr/local/texlive/2009/texmf-dist/tex/latex/amsfonts/umsa.fd File: umsa.fd 2009/06/22 v3.00 AMS symbols A ) LaTeX Font Info: Try loading font information for U+msb on input line 119. (/usr/local/texlive/2009/texmf-dist/tex/latex/amsfonts/umsb.fd File: umsb.fd 2009/06/22 v3.00 AMS symbols B ) [1{/usr/local/texlive/2009/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] [2] LaTeX Font Info: Font shape `OT1/ppl/bx/n' in size <10.95> not available (Font) Font shape `OT1/ppl/b/n' tried instead on input line 124. Overfull \hbox (24.72739pt too wide) in paragraph at lines 139--143 []\OT1/ppl/m/n/12 Markov mod-els pro-vide a way to model the slow con-for-ma-ti onal dy-nam-ics of biomolecules [] [3] [4] [5] [6] LaTeX Font Info: Font shape `OT1/ppl/bx/n' in size <12> not available (Font) Font shape `OT1/ppl/b/n' tried instead on input line 212. Package natbib Warning: Citation `Voter:1985p2344' on page 7 undefined on input line 212. ! Misplaced alignment tab character &. l.212 ...ter:1985p2344}{\color{red}[CITE: Straub & Doll ?]}. While $\bfm{T}(... ? ! Emergency stop. l.212 ...ter:1985p2344}{\color{red}[CITE: Straub & Doll ?]}. While $\bfm{T}(... End of file on the terminal! Here is how much of TeX's memory you used: 7343 strings out of 493848 104492 string characters out of 3149206 195013 words of memory out of 3000000 10427 multiletter control sequences out of 15000+200000 19957 words of font info for 60 fonts, out of 3000000 for 9000 714 hyphenation exceptions out of 8191 34i,12n,28p,1729b,368s stack positions out of 5000i,500n,10000p,200000b,50000s ! ==> Fatal error occurred, no output PDF file produced!