This is TeX, Version 3.14159 (Web2C 7.4.5) (format=latex 2003.9.1)  6 OCT 2009 11:19
**nMOLDYN_for_HTML.tex
(./nMOLDYN_for_HTML.tex
LaTeX2e <2001/06/01>
Babel <v3.7h> and hyphenation patterns for american, french, german, ngerman, n
ohyphenation, loaded.
(/usr/share/texmf/tex/latex/base/report.cls
Document Class: report 2001/04/21 v1.4e Standard LaTeX document class
(/usr/share/texmf/tex/latex/base/size11.clo
File: size11.clo 2001/04/21 v1.4e Standard LaTeX file (size option)
)
\c@part=\count79
\c@chapter=\count80
\c@section=\count81
\c@subsection=\count82
\c@subsubsection=\count83
\c@paragraph=\count84
\c@subparagraph=\count85
\c@figure=\count86
\c@table=\count87
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
)
(/usr/share/texmf/tex/latex/tools/array.sty
Package: array 1998/05/13 v2.3m Tabular extension package (FMi)
\col@sep=\dimen103
\extrarowheight=\dimen104
\NC@list=\toks14
\extratabsurround=\skip43
\backup@length=\skip44
)
(/usr/share/texmf/tex/latex/base/makeidx.sty
Package: makeidx 2000/03/29 v1.0m Standard LaTeX package
)
(/usr/share/texmf/tex/latex/preprint/fullpage.sty
Package: fullpage 1999/02/23 1.1 (PWD)
\FP@margin=\skip45
)
(/usr/share/texmf/tex/latex/graphics/graphicx.sty
Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)

(/usr/share/texmf/tex/latex/graphics/keyval.sty
Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
\KV@toks@=\toks15
)
(/usr/share/texmf/tex/latex/graphics/graphics.sty
Package: graphics 2001/07/07 v1.0n Standard LaTeX Graphics (DPC,SPQR)

(/usr/share/texmf/tex/latex/graphics/trig.sty
Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
)
(/usr/share/texmf/tex/latex/config/graphics.cfg
File: graphics.cfg 2001/08/31 v1.1 graphics configuration of teTeX/TeXLive
)
Package graphics Info: Driver file: dvips.def on input line 80.

(/usr/share/texmf/tex/latex/graphics/dvips.def
File: dvips.def 1999/02/16 v3.0i Driver-dependant file (DPC,SPQR)
))
\Gin@req@height=\dimen105
\Gin@req@width=\dimen106
) (./appendix.sty
Package: appendix 2002/08/06 v1.2 extra appendix facilities
\c@@pps=\count88
\c@@ppsavesec=\count89
\c@@ppsaveapp=\count90
)
(./glossary.sty
Package: glossary 2006/07/20 2.4 (NLCT)
 (/usr/share/texmf/tex/latex/base/ifthen.sty
Package: ifthen 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)
)
\gls@cols=\count91

No configuration file glossary.cfg found
(/usr/share/texmf/tex/latex/tools/longtable.sty
Package: longtable 2000/10/22 v4.10 Multi-page Table package (DPC)
\LTleft=\skip46
\LTright=\skip47
\LTpre=\skip48
\LTpost=\skip49
\LTchunksize=\count92
\LTcapwidth=\dimen107
\LT@head=\box26
\LT@firsthead=\box27
\LT@foot=\box28
\LT@lastfoot=\box29
\LT@cols=\count93
\LT@rows=\count94
\c@LT@tables=\count95
\c@LT@chunks=\count96
\LT@p@ftn=\toks16
)
\descriptionwidth=\skip50
\istfile=\write3
)
\@acronymfile=\write4
\openout4 = `nMOLDYN_for_HTML.acr'.


Writing acronym file nMOLDYN_for_HTML.acr 
(./nMOLDYN_for_HTML.aux

LaTeX Warning: Label `eq:q_dual' multiply defined.


LaTeX Warning: Label `nmoldyn_input_files' multiply defined.

)
\openout1 = `nMOLDYN_for_HTML.aux'.

LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 76.
LaTeX Font Info:    ... okay on input line 76.
LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 76.
LaTeX Font Info:    ... okay on input line 76.
LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 76.
LaTeX Font Info:    ... okay on input line 76.
LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 76.
LaTeX Font Info:    ... okay on input line 76.
LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 76.
LaTeX Font Info:    ... okay on input line 76.
LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 76.
LaTeX Font Info:    ... okay on input line 76.
File: ./Figures/logo.eps Graphic file (type eps)
 <./Figures/logo.eps>
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <14.4> on input line 94.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <7> on input line 94.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <10.95> on input line 112.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <8> on input line 112.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <6> on input line 112.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <9> on input line 116.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <5> on input line 116.
 [1

\openout3 = `nMOLDYN_for_HTML.ist'.

] [1] (./nMOLDYN_for_HTML.toc [1

]
Underfull \hbox (badness 10000) in paragraph at lines 119--119
 []  
 []

[2])
\tf@toc=\write5
\openout5 = `nMOLDYN_for_HTML.toc'.

 [3] (./nMOLDYN_for_HTML.lof [4

])
\tf@lof=\write6
\openout6 = `nMOLDYN_for_HTML.lof'.

 [5] (./nMOLDYN_for_HTML.lot)
\tf@lot=\write7
\openout7 = `nMOLDYN_for_HTML.lot'.

 [6

]
(./nMOLDYN_for_HTML.acn
Overfull \hbox (185.03082pt too wide) in alignment at lines 1--1
 [] [] 
 []


Overfull \hbox (185.03082pt too wide) in alignment at lines 1--1
 [] [] 
 []


Overfull \hbox (185.03082pt too wide) in alignment at lines 1--91
 [] [] 
 []


Overfull \hbox (185.03082pt too wide) in alignment at lines 91--194
 [] [] 
 []


Overfull \hbox (185.03082pt too wide) in alignment at lines 194--260
 [] [] 
 []

[7

]
Overfull \hbox (185.03082pt too wide) in alignment at lines 260--265
 [] [] 
 []

) [8]
Chapter 1.
[9

]
LaTeX Font Info:    Try loading font information for OMS+cmr on input line 222.

 (/usr/share/texmf/tex/latex/base/omscmr.fd
File: omscmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions
)
LaTeX Font Info:    Font shape `OMS/cmr/m/n' in size <10.95> not available
(Font)              Font shape `OMS/cmsy/m/n' tried instead on input line 222.
 [10] [11]
Chapter 2.

Underfull \hbox (badness 10000) in paragraph at lines 321--326

 []


Underfull \hbox (badness 10000) in paragraph at lines 321--326

 []


Underfull \hbox (badness 10000) in paragraph at lines 327--328

 []


Underfull \hbox (badness 10000) in paragraph at lines 328--329

 []


Underfull \hbox (badness 10000) in paragraph at lines 329--330

 []

[12

]
Underfull \hbox (badness 10000) in paragraph at lines 330--331

 []


Underfull \hbox (badness 10000) in paragraph at lines 336--343

 []


Underfull \hbox (badness 10000) in paragraph at lines 336--343

 []

[13]
Chapter 3.
[14

] [15]
Chapter 4.
LaTeX Font Info:    Try loading font information for OMS+cmtt on input line 442
.
LaTeX Font Info:    No file OMScmtt.fd. on input line 442.

LaTeX Font Warning: Font shape `OMS/cmtt/m/n' undefined
(Font)              using `OMS/cmsy/m/n' instead
(Font)              for symbol `textbackslash' on input line 442.


Underfull \hbox (badness 10000) in paragraph at lines 427--447

 []


Underfull \hbox (badness 10000) in paragraph at lines 427--447

 []


Underfull \hbox (badness 10000) in paragraph at lines 427--447

 []


Underfull \hbox (badness 10000) in paragraph at lines 427--447

 []

[16

]
Overfull \hbox (3.93631pt too wide) in paragraph at lines 463--468
\OT1/cmr/bx/n/10.95 Description: \OT1/cmr/m/n/10.95 runs an anal-y-sis with the
 command-line in-ter-face us-ing \OT1/cmr/m/it/10.95 file-name n\OT1/cmr/m/n/10
.95 MOLDYN
 []


Underfull \hbox (badness 10000) in paragraph at lines 477--487

 []


Underfull \hbox (badness 10000) in paragraph at lines 477--487

 []

[17] [18] [19]
File: Figures/main_dialog.eps Graphic file (type eps)
 <Figures/main_dialog.eps> [20]
File: Figures/file_browser.eps Graphic file (type eps)
 <Figures/file_browser.eps>
File: Figures/trajectory_set.eps Graphic file (type eps)

<Figures/trajectory_set.eps> [21] [22]
File: Figures/amber_converter.eps Graphic file (type eps)
 <Figures/amber_converter.eps>
File: Figures/charmm_converter.eps Graphic file (type eps)

<Figures/charmm_converter.eps> [23] [24]
File: Figures/dlpoly_converter.eps Graphic file (type eps)
 <Figures/dlpoly_converter.eps>
[25]
File: Figures/dlpoly_field_example.eps Graphic file (type eps)
 <Figures/dlpoly_field_example.eps>
Underfull \hbox (badness 10000) in paragraph at lines 785--793

 []


Underfull \hbox (badness 10000) in paragraph at lines 785--793

 []

[26]
File: Figures/discover_converter.eps Graphic file (type eps)
 <Figures/discover_converter.eps>
Overfull \hbox (5.32971pt too wide) in paragraph at lines 842--848
\OT1/cmr/m/n/10.95 where \OT1/cmr/m/it/10.95 sep \OT1/cmr/m/n/10.95 can be a wh
ite space, a comma or a semi-colon and each block \OT1/cmr/m/it/10.95 mini:maxi
:skipi
 []

[27]
File: Figures/forcite_converter.eps Graphic file (type eps)
 <Figures/forcite_converter.eps> [28]
Overfull \hbox (17.41838pt too wide) in paragraph at lines 899--903
\OT1/cmr/m/n/10.95 where \OT1/cmr/m/it/10.95 sep \OT1/cmr/m/n/10.95 can be a wh
ite space, a comma or a semi-colon and each block \OT1/cmr/m/it/10.95 min[]i:ma
x[]i:skip[]i
 []

[29]
File: Figures/namd_converter.eps Graphic file (type eps)
 <Figures/namd_converter.eps>
File: Figures/vasp_converter.eps Graphic file (type eps)
 <Figures/vasp_converter.eps>
Overfull \hbox (10.11859pt too wide) in paragraph at lines 954--963
\OT1/cmr/m/n/10.95 This con-verter al-lows the con-ver-sion from a tra-jec-tory
 gen-er-ated with \OT1/cmr/bx/n/10.95 V\OT1/cmr/m/n/10.95 ienna \OT1/cmr/bx/n/1
0.95 A\OT1/cmr/m/n/10.95 b-initio \OT1/cmr/bx/n/10.95 S\OT1/cmr/m/n/10.95 imula
tion
 []


LaTeX Warning: `!h' float specifier changed to `!ht'.

[30]
Underfull \hbox (badness 10000) in paragraph at lines 983--990

 []


Underfull \hbox (badness 10000) in paragraph at lines 983--990

 []

File: Figures/frame_snapshot.eps Graphic file (type eps)
<Figures/frame_snapshot.eps> [31]
Underfull \hbox (badness 10000) in paragraph at lines 1031--1039

 []


Underfull \hbox (badness 10000) in paragraph at lines 1031--1039

 []

[32]
File: Figures/convert_netcdf_ascii.eps Graphic file (type eps)
 <Figures/convert_netcdf_ascii.eps> [33]
Underfull \hbox (badness 10000) in paragraph at lines 1083--1087

 []

[34]
File: Figures/convert_ascii_netcdf.eps Graphic file (type eps)
 <Figures/convert_ascii_netcdf.eps>
Underfull \hbox (badness 10000) in paragraph at lines 1108--1128

 []


Underfull \hbox (badness 10000) in paragraph at lines 1108--1128

 []


Underfull \hbox (badness 10000) in paragraph at lines 1108--1128

 []


Underfull \hbox (badness 10000) in paragraph at lines 1108--1128

 []

[35]
File: Figures/convert_ascii_netcdf_example.eps Graphic file (type eps)
 <Figures/convert_ascii_netcdf_example.eps>
File: Figures/preferences_file_handling.eps Graphic file (type eps)

<Figures/preferences_file_handling.eps> [36]
File: Figures/preferences_file_handling.eps Graphic file (type eps)

<Figures/preferences_file_handling.eps>
File: Figures/preferences_external_programs.eps Graphic file (type eps)

<Figures/preferences_external_programs.eps>
File: Figures/preferences_miscellaneous.eps Graphic file (type eps)

<Figures/preferences_miscellaneous.eps> [37] [38] [39]
Underfull \hbox (badness 10000) in paragraph at lines 1303--1317

 []


Underfull \hbox (badness 10000) in paragraph at lines 1303--1317

 []


Underfull \hbox (badness 10000) in paragraph at lines 1303--1317

 []


Underfull \hbox (badness 10000) in paragraph at lines 1303--1317

 []

[40]
File: Figures/preferences_config_file_example.eps Graphic file (type eps)
 <Figures/preferences_config_file_example.eps> [41] [42] [43]
File: Figures/subset_selection.eps Graphic file (type eps)

<Figures/subset_selection.eps> [44]
File: Figures/subset_selection_from_a_selection_file.eps Graphic file (type eps
)

<Figures/subset_selection_from_a_selection_file.eps>
File: Figures/subset_selection_file.eps Graphic file (type eps)

<Figures/subset_selection_file.eps>
File: Figures/subset_selection_from_the_loaded_trajectory.eps Graphic file (typ
e eps)

<Figures/subset_selection_from_the_loaded_trajectory.eps> [45]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1543

 []


Underfull \hbox (badness 10000) in paragraph at lines 1536--1543

 []


Underfull \hbox (badness 10000) in paragraph at lines 1544--1551

 []


Underfull \hbox (badness 10000) in paragraph at lines 1544--1551

 []


Underfull \hbox (badness 10000) in paragraph at lines 1552--1560

 []


Underfull \hbox (badness 10000) in paragraph at lines 1552--1560

 []

[46] [47]
File: Figures/subset_selection_from_an_expression_string.eps Graphic file (type
 eps)
 <Figures/subset_selection_from_an_expression_string.eps> [48]
File: Figures/deuteration_selection.eps Graphic file (type eps)

<Figures/deuteration_selection.eps> [49]
File: Figures/deuteration_selection_from_a_selection_file.eps Graphic file (typ
e eps)

<Figures/deuteration_selection_from_a_selection_file.eps>
File: Figures/deuteration_selection_file.eps Graphic file (type eps)

<Figures/deuteration_selection_file.eps> [50]
File: Figures/deuteration_selection_from_the_loaded_trajectory.eps Graphic file
 (type eps)

<Figures/deuteration_selection_from_the_loaded_trajectory.eps>
Underfull \hbox (badness 10000) in paragraph at lines 1754--1761

 []


Underfull \hbox (badness 10000) in paragraph at lines 1754--1761

 []


Underfull \hbox (badness 10000) in paragraph at lines 1762--1769

 []


Underfull \hbox (badness 10000) in paragraph at lines 1762--1769

 []


Underfull \hbox (badness 10000) in paragraph at lines 1770--1778

 []


Underfull \hbox (badness 10000) in paragraph at lines 1770--1778

 []

[51]
File: Figures/deuteration_selection_from_an_expression_string.eps Graphic file 
(type eps)
 <Figures/deuteration_selection_from_an_expression_string.eps> [52]
File: Figures/group_selection.eps Graphic file (type eps)

<Figures/group_selection.eps> [53]
File: Figures/group_selection_from_a_selection_file.eps Graphic file (type eps)


<Figures/group_selection_from_a_selection_file.eps>
File: Figures/group_selection_file.eps Graphic file (type eps)

<Figures/group_selection_file.eps> [54]
File: Figures/group_selection_from_the_loaded_trajectory.eps Graphic file (type
 eps)

<Figures/group_selection_from_the_loaded_trajectory.eps> [55]
Underfull \hbox (badness 10000) in paragraph at lines 1894--1900

 []


Underfull \hbox (badness 10000) in paragraph at lines 1894--1900

 []


Underfull \hbox (badness 10000) in paragraph at lines 1901--1908

 []


Overfull \hbox (62.29646pt too wide) in paragraph at lines 1901--1908
\OT1/cmr/m/it/10.95 group1 group-in-glevel level ob-ject-name name key-word1 va
lue1,value2,...OR key-word2, value1,value2,value3... 
 []


Underfull \hbox (badness 10000) in paragraph at lines 1901--1908

 []


Underfull \hbox (badness 10000) in paragraph at lines 1909--1917

 []


Underfull \hbox (badness 10000) in paragraph at lines 1909--1917

 []

[56]
File: Figures/group_selection_from_an_expression_string.eps Graphic file (type 
eps)
 <Figures/group_selection_from_an_expression_string.eps> [57] [58]
File: Figures/msd_water.eps Graphic file (type eps)

<Figures/msd_water.eps> [59] [60]
File: Figures/msd.eps Graphic file (type eps)
 <Figures/msd.eps>
Underfull \hbox (badness 10000) in paragraph at lines 2146--2156

 []


Underfull \hbox (badness 10000) in paragraph at lines 2146--2156

 []

[61]
Underfull \hbox (badness 10000) in paragraph at lines 2163--2173

 []


Underfull \hbox (badness 10000) in paragraph at lines 2163--2173

 []

[62]
File: Figures/rmsd.eps Graphic file (type eps)
 <Figures/rmsd.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 2251--2261

 []


Underfull \hbox (badness 10000) in paragraph at lines 2251--2261

 []

[63] [64] [65]
File: Figures/rog.eps Graphic file (type eps)
 <Figures/rog.eps>
Underfull \hbox (badness 10000) in paragraph at lines 2353--2363

 []


Underfull \hbox (badness 10000) in paragraph at lines 2353--2363

 []

[66] [67]
File: Figures/ac.eps Graphic file (type eps)
 <Figures/ac.eps>
Underfull \hbox (badness 10000) in paragraph at lines 2456--2466

 []


Underfull \hbox (badness 10000) in paragraph at lines 2456--2466

 []

[68]
Underfull \hbox (badness 10000) in paragraph at lines 2480--2488

 []

[69] [70]
File: Figures/vacf.eps Graphic file (type eps)
 <Figures/vacf.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 2593--2603

 []


Underfull \hbox (badness 10000) in paragraph at lines 2593--2603

 []

[71] [72]
Underfull \hbox (badness 10000) in paragraph at lines 2627--2637

 []


Underfull \hbox (badness 10000) in paragraph at lines 2627--2637

 []

[73]
File: Figures/dos.eps Graphic file (type eps)
 <Figures/dos.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 2716--2726

 []


Underfull \hbox (badness 10000) in paragraph at lines 2716--2726

 []

[74]
Underfull \hbox (badness 10000) in paragraph at lines 2750--2760

 []


Underfull \hbox (badness 10000) in paragraph at lines 2750--2760

 []

[75] [76]
File: Figures/pbft.eps Graphic file (type eps)
 <Figures/pbft.eps>
Underfull \hbox (badness 10000) in paragraph at lines 2835--2845

 []


Underfull \hbox (badness 10000) in paragraph at lines 2835--2845

 []

[77]
Underfull \hbox (badness 10000) in paragraph at lines 2852--2861

 []


Underfull \hbox (badness 10000) in paragraph at lines 2852--2861

 []

[78] [79]
File: Figures/gmft.eps Graphic file (type eps)
 <Figures/gmft.eps>
Underfull \hbox (badness 10000) in paragraph at lines 2919--2929

 []


Underfull \hbox (badness 10000) in paragraph at lines 2919--2929

 []

[80] [81] [82]
File: Figures/rbt.eps Graphic file (type eps)
 <Figures/rbt.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 3161--3171

 []


Underfull \hbox (badness 10000) in paragraph at lines 3161--3171

 []

[83] [84] [85]
File: Figures/comt.eps Graphic file (type eps)
 <Figures/comt.eps>
Underfull \hbox (badness 10000) in paragraph at lines 3251--3261

 []


Underfull \hbox (badness 10000) in paragraph at lines 3251--3261

 []

[86] [87] [88] [89] [90]
File: Figures/ara.eps Graphic file (type eps)
 <Figures/ara.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 3540--3550

 []


Underfull \hbox (badness 10000) in paragraph at lines 3540--3550

 []

[91] [92]
Underfull \hbox (badness 10000) in paragraph at lines 3574--3584

 []


Underfull \hbox (badness 10000) in paragraph at lines 3574--3584

 []

[93] [94] [95]
File: Figures/qha.eps Graphic file (type eps)
 <Figures/qha.eps>
Underfull \hbox (badness 10000) in paragraph at lines 3753--3763

 []


Underfull \hbox (badness 10000) in paragraph at lines 3753--3763

 []

[96] [97] [98] [99]
File: Figures/rcf.eps Graphic file (type eps)
 <Figures/rcf.eps>
Overfull \hbox (10.33623pt too wide) in paragraph at lines 3946--3947
[]\OT1/cmr/m/n/10.95 The fol-low-ing in-put fields con-trols the pa-ram-e-ters 
for the \OT1/cmr/bx/n/10.95 R\OT1/cmr/m/n/10.95 eorientational \OT1/cmr/bx/n/10
.95 C\OT1/cmr/m/n/10.95 orrelation \OT1/cmr/bx/n/10.95 F\OT1/cmr/m/n/10.95 unct
ion
 []


Underfull \hbox (badness 10000) in paragraph at lines 3955--3965

 []


Underfull \hbox (badness 10000) in paragraph at lines 3955--3965

 []

[100]
Underfull \hbox (badness 10000) in paragraph at lines 3985--3994

 []


Underfull \hbox (badness 10000) in paragraph at lines 3985--3994

 []

[101]
File: Figures/avacf.eps Graphic file (type eps)
 <Figures/avacf.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 4088--4098

 []


Underfull \hbox (badness 10000) in paragraph at lines 4088--4098

 []

[102]
Underfull \hbox (badness 10000) in paragraph at lines 4122--4132

 []


Underfull \hbox (badness 10000) in paragraph at lines 4122--4132

 []

[103]
File: Figures/ados.eps Graphic file (type eps)
 <Figures/ados.eps> [104]
Underfull \hbox (badness 10000) in paragraph at lines 4192--4202

 []


Underfull \hbox (badness 10000) in paragraph at lines 4192--4202

 []

[105]
Underfull \hbox (badness 10000) in paragraph at lines 4226--4236

 []


Underfull \hbox (badness 10000) in paragraph at lines 4226--4236

 []

[106]
Underfull \hbox (badness 10000) in paragraph at lines 4291--4291

 []

[107] [108] [109]
Overfull \hbox (54.36754pt too wide) detected at line 4444
[]\OMS/cmtt/m/n/10.95 F[]\OT1/cmr/m/n/10.95 (\OML/cmm/m/it/10.95 q[]; k \OMS/cm
tt/m/n/10.95 ^^A \OT1/cmr/m/n/10.95 ^^A\OML/cmm/m/it/10.95 t\OT1/cmr/m/n/10.95 
) [] [] [][][]\OML/cmm/m/it/10.95 ;  k \OT1/cmr/m/n/10.95 = 0 [] \OML/cmm/m/it/
10.95 N[] \OMS/cmtt/m/n/10.95 ^^@ \OT1/cmr/m/n/10.95 1\OML/cmm/m/it/10.95 ;  m 
\OT1/cmr/m/n/10.95 = 0 [] \OML/cmm/m/it/10.95 N[] \OMS/cmtt/m/n/10.95 ^^@ \OT1/
cmr/m/n/10.95 1\OML/cmm/m/it/10.95 :
 []

[110] [111]
File: Figures/dcsf.eps Graphic file (type eps)
 <Figures/dcsf.eps>
Underfull \hbox (badness 10000) in paragraph at lines 4509--4519

 []


Underfull \hbox (badness 10000) in paragraph at lines 4509--4519

 []

[112]
Underfull \hbox (badness 10000) in paragraph at lines 4526--4539

 []


Underfull \hbox (badness 10000) in paragraph at lines 4526--4539

 []

[113]
Underfull \hbox (badness 10000) in paragraph at lines 4581--4588

 []


Underfull \hbox (badness 10000) in paragraph at lines 4581--4588

 []


Underfull \hbox (badness 10000) in paragraph at lines 4589--4595

 []


Underfull \hbox (badness 10000) in paragraph at lines 4589--4595

 []

[114] [115] [116]
File: Figures/dcsfar.eps Graphic file (type eps)
 <Figures/dcsfar.eps>
Underfull \hbox (badness 10000) in paragraph at lines 4702--4712

 []


Underfull \hbox (badness 10000) in paragraph at lines 4702--4712

 []

[117]
Underfull \hbox (badness 10000) in paragraph at lines 4727--4740

 []


Underfull \hbox (badness 10000) in paragraph at lines 4727--4740

 []

[118]
Underfull \hbox (badness 10000) in paragraph at lines 4782--4788

 []


Underfull \hbox (badness 10000) in paragraph at lines 4782--4788

 []


Underfull \hbox (badness 10000) in paragraph at lines 4789--4795

 []


Underfull \hbox (badness 10000) in paragraph at lines 4789--4795

 []

[119] [120]
File: Figures/disf.eps Graphic file (type eps)
 <Figures/disf.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.

[121]
Underfull \hbox (badness 10000) in paragraph at lines 4917--4927

 []


Underfull \hbox (badness 10000) in paragraph at lines 4917--4927

 []

[122]
Underfull \hbox (badness 10000) in paragraph at lines 4934--4947

 []


Underfull \hbox (badness 10000) in paragraph at lines 4934--4947

 []

[123]
Underfull \hbox (badness 10000) in paragraph at lines 4989--4995

 []


Underfull \hbox (badness 10000) in paragraph at lines 4989--4995

 []


Underfull \hbox (badness 10000) in paragraph at lines 4996--5002

 []


Underfull \hbox (badness 10000) in paragraph at lines 4996--5002

 []

[124] [125]
File: Figures/disfar.eps Graphic file (type eps)
 <Figures/disfar.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 5107--5117

 []


Underfull \hbox (badness 10000) in paragraph at lines 5107--5117

 []

[126]
Underfull \hbox (badness 10000) in paragraph at lines 5132--5145

 []


Underfull \hbox (badness 10000) in paragraph at lines 5132--5145

 []

[127]
Underfull \hbox (badness 10000) in paragraph at lines 5187--5193

 []


Underfull \hbox (badness 10000) in paragraph at lines 5187--5193

 []

[128]
Underfull \hbox (badness 10000) in paragraph at lines 5194--5200

 []


Underfull \hbox (badness 10000) in paragraph at lines 5194--5200

 []

[129] [130]
File: Figures/disfg.eps Graphic file (type eps)
 <Figures/disfg.eps> [131]
Underfull \hbox (badness 10000) in paragraph at lines 5319--5329

 []


Underfull \hbox (badness 10000) in paragraph at lines 5319--5329

 []


Underfull \hbox (badness 10000) in paragraph at lines 5336--5349

 []


Underfull \hbox (badness 10000) in paragraph at lines 5336--5349

 []

[132] [133]
File: Figures/eisf.eps Graphic file (type eps)
 <Figures/eisf.eps> [134]
Underfull \hbox (badness 10000) in paragraph at lines 5499--5509

 []


Underfull \hbox (badness 10000) in paragraph at lines 5499--5509

 []

[135]
Underfull \hbox (badness 10000) in paragraph at lines 5516--5529

 []


Underfull \hbox (badness 10000) in paragraph at lines 5516--5529

 []

[136]
Underfull \hbox (badness 10000) in paragraph at lines 5571--5577

 []


Underfull \hbox (badness 10000) in paragraph at lines 5571--5577

 []


Underfull \hbox (badness 10000) in paragraph at lines 5578--5584

 []


Underfull \hbox (badness 10000) in paragraph at lines 5578--5584

 []

[137]
File: Figures/scsf.eps Graphic file (type eps)
 <Figures/scsf.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 5656--5666

 []


Underfull \hbox (badness 10000) in paragraph at lines 5656--5666

 []

[138]
Underfull \hbox (badness 10000) in paragraph at lines 5673--5686

 []


Underfull \hbox (badness 10000) in paragraph at lines 5673--5686

 []

[139]
Underfull \hbox (badness 10000) in paragraph at lines 5728--5734

 []


Underfull \hbox (badness 10000) in paragraph at lines 5728--5734

 []

[140]
Underfull \hbox (badness 10000) in paragraph at lines 5735--5741

 []


Underfull \hbox (badness 10000) in paragraph at lines 5735--5741

 []

[141]
File: Figures/sscsf.eps Graphic file (type eps)
 <Figures/sscsf.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 5828--5838

 []


Underfull \hbox (badness 10000) in paragraph at lines 5828--5838

 []

[142]
Underfull \hbox (badness 10000) in paragraph at lines 5845--5858

 []


Underfull \hbox (badness 10000) in paragraph at lines 5845--5858

 []

[143] [144]
File: Figures/pdf.eps Graphic file (type eps)
 <Figures/pdf.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 5975--5985

 []


Underfull \hbox (badness 10000) in paragraph at lines 5975--5985

 []

[145]
Underfull \hbox (badness 10000) in paragraph at lines 5992--6006

 []


Underfull \hbox (badness 10000) in paragraph at lines 5992--6006

 []

[146] [147]
Overfull \hbox (16.05159pt too wide) detected at line 6073
[]\OML/cmm/m/it/10.95 CN\OT1/cmr/m/n/10.95 (\OML/cmm/m/it/10.95 r[]\OT1/cmr/m/n
/10.95 ) [] [][] [] [] [] \OML/cmm/m/it/10.95 CN[]\OT1/cmr/m/n/10.95 (\OML/cmm/
m/it/10.95 r[]; t[]\OT1/cmr/m/n/10.95 )\OML/cmm/m/it/10.95 ;  m \OT1/cmr/m/n/10
.95 = 0 [] \OML/cmm/m/it/10.95 N[] \OMS/cmtt/m/n/10.95 ^^@ \OT1/cmr/m/n/10.95 1
\OML/cmm/m/it/10.95 ;  n \OT1/cmr/m/n/10.95 = 0 [] \OML/cmm/m/it/10.95 N[] \OMS
/cmtt/m/n/10.95 ^^@ \OT1/cmr/m/n/10.95 1\OML/cmm/m/it/10.95 :
 []

File: Figures/cn.eps Graphic file (type eps)
<Figures/cn.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 6109--6119

 []


Underfull \hbox (badness 10000) in paragraph at lines 6109--6119

 []

[148]
Underfull \hbox (badness 10000) in paragraph at lines 6126--6140

 []


Underfull \hbox (badness 10000) in paragraph at lines 6126--6140

 []

[149] [150] [151]
Overfull \hbox (96.5633pt too wide) detected at line 6213
[]\OML/cmm/m/it/10.95 SD\OT1/cmr/m/n/10.95 (\OML/cmm/m/it/10.95 r[]; ^^R[]; ^^^
[]\OT1/cmr/m/n/10.95 ) [] [] [] [] [] \OML/cmm/m/it/10.95 ;  l \OT1/cmr/m/n/10.
95 = 0 [] \OML/cmm/m/it/10.95 N[] \OMS/cmtt/m/n/10.95 ^^@ \OT1/cmr/m/n/10.95 1\
OML/cmm/m/it/10.95 ; m \OT1/cmr/m/n/10.95 = 0 [] \OML/cmm/m/it/10.95 N[] \OMS/c
mtt/m/n/10.95 ^^@ \OT1/cmr/m/n/10.95 1\OML/cmm/m/it/10.95 ; n \OT1/cmr/m/n/10.9
5 = 0 [] \OML/cmm/m/it/10.95 N[] \OMS/cmtt/m/n/10.95 ^^@ \OT1/cmr/m/n/10.95 1\O
ML/cmm/m/it/10.95 :
 []

[152]
File: Figures/sd.eps Graphic file (type eps)
 <Figures/sd.eps>
Underfull \hbox (badness 10000) in paragraph at lines 6260--6270

 []


Underfull \hbox (badness 10000) in paragraph at lines 6260--6270

 []

[153]
Underfull \hbox (badness 10000) in paragraph at lines 6277--6291

 []


Underfull \hbox (badness 10000) in paragraph at lines 6277--6291

 []

[154]
Underfull \hbox (badness 10000) in paragraph at lines 6298--6312

 []


Underfull \hbox (badness 10000) in paragraph at lines 6298--6312

 []


Underfull \hbox (badness 10000) in paragraph at lines 6313--6327

 []


Underfull \hbox (badness 10000) in paragraph at lines 6313--6327

 []


Underfull \hbox (badness 10000) in paragraph at lines 6335--6343

 []

[155] [156]
File: Figures/sfa.eps Graphic file (type eps)
 <Figures/sfa.eps>
Underfull \hbox (badness 10000) in paragraph at lines 6409--6419

 []


Underfull \hbox (badness 10000) in paragraph at lines 6409--6419

 []

[157] [158]
File: Figures/op.eps Graphic file (type eps)
 <Figures/op.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 6527--6537

 []


Underfull \hbox (badness 10000) in paragraph at lines 6527--6537

 []

[159]
Underfull \hbox (badness 10000) in paragraph at lines 6550--6558

 []

[160]
File: Figures/opcm.eps Graphic file (type eps)
 <Figures/opcm.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.


Underfull \hbox (badness 10000) in paragraph at lines 6622--6632

 []


Underfull \hbox (badness 10000) in paragraph at lines 6622--6632

 []

[161] [162]
File: Figures/plot.eps Graphic file (type eps)
 <Figures/plot.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.

File: Figures/matplotlib_home.eps Graphic file (type eps)
<Figures/matplotlib_home.eps> [163]
File: Figures/matplotlib_back.eps Graphic file (type eps)
 <Figures/matplotlib_back.eps>
File: Figures/matplotlib_forward.eps Graphic file (type eps)

<Figures/matplotlib_forward.eps>
File: Figures/matplotlib_move.eps Graphic file (type eps)
 <Figures/matplotlib_move.eps> [164]
File: Figures/matplotlib_zoom_to_rect.eps Graphic file (type eps)

<Figures/matplotlib_zoom_to_rect.eps>
File: Figures/matplotlib_subplots.eps Graphic file (type eps)
 <Figures/matplotlib_subplots.eps>
File: Figures/matplotlib_filesave.eps Graphic file (type eps)

<Figures/matplotlib_filesave.eps>
File: Figures/plot_settings.eps Graphic file (type eps)
 <Figures/plot_settings.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.

[165]
File: Figures/export_plot.eps Graphic file (type eps)
 <Figures/export_plot.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.

File: Figures/animation.eps Graphic file (type eps)
<Figures/animation.eps>

LaTeX Warning: `!h' float specifier changed to `!ht'.

[166] [167]
File: Figures/effective_mode_viewer.eps Graphic file (type eps)
 <Figures/effective_mode_viewer.eps> [168]
Underfull \hbox (badness 10000) in paragraph at lines 6887--6892

 []


Underfull \hbox (badness 10000) in paragraph at lines 6887--6892

 []

[169] [170]
File: Figures/benchmark.eps Graphic file (type eps)
 <Figures/benchmark.eps> [171]
File: Figures/about_nmoldyn.eps Graphic file (type eps)
 <Figures/about_nmoldyn.eps> [172]
Chapter 5.

Underfull \hbox (badness 10000) in paragraph at lines 6957--6969

 []


Underfull \hbox (badness 10000) in paragraph at lines 6957--6969

 []


Underfull \hbox (badness 10000) in paragraph at lines 6957--6969

 []


Underfull \hbox (badness 10000) in paragraph at lines 6957--6969

 []


Underfull \hbox (badness 10000) in paragraph at lines 6970--6984

 []


Underfull \hbox (badness 10000) in paragraph at lines 6970--6984

 []


Underfull \hbox (badness 10000) in paragraph at lines 6970--6984

 []


Underfull \hbox (badness 10000) in paragraph at lines 6970--6984

 []


Underfull \hbox (badness 10000) in paragraph at lines 6970--6984

 []


Underfull \hbox (badness 10000) in paragraph at lines 6970--6984

 []


Underfull \hbox (badness 10000) in paragraph at lines 6970--6984

 []


Underfull \hbox (badness 10000) in paragraph at lines 6970--6984

 []

[173

] [174]
File: Figures/msd_autostart_file.eps Graphic file (type eps)
 <Figures/msd_autostart_file.eps> [175]
Overfull \hbox (6.05733pt too wide) in paragraph at lines 7027--7027
[]|\OT1/cmr/m/n/10.95 CartesianVelocityAutoCorrelationFunction[]serial| 
 []


Underfull \hbox (badness 1400) in paragraph at lines 7043--7043
[]|\OT1/cmr/m/n/10.95 Reorientational Cor-re-la-tion Func-
 []


Underfull \hbox (badness 1009) in paragraph at lines 7045--7045
[]|\OT1/cmr/m/n/10.95 Angular Ve-loc-ity Au-to-Cor-re-la-tion
 []


Overfull \hbox (13.67673pt too wide) in paragraph at lines 7057--7057
[]|\OT1/cmr/m/n/10.95 DynamicIncoherentStructureFactorGaussian[]serial| 
 []


Overfull \hbox (19.47069pt too wide) in paragraph at lines 7015--7078
 [][] 
 []

[176]
Overfull \hbox (10.76477pt too wide) in paragraph at lines 7084--7096
\OT1/cmr/m/n/10.95 The \OT1/cmr/m/it/10.95 n\OT1/cmr/m/n/10.95 MOLDYN in-put fi
les (ex-ten-sion \OT1/cmr/bx/n/10.95 .nmi\OT1/cmr/m/n/10.95 ) are ASCII files t
hat must be run through \OT1/cmr/m/it/10.95 n\OT1/cmr/m/n/10.95 MOLDYN.
 []


Underfull \hbox (badness 10000) in paragraph at lines 7084--7096

 []


Underfull \hbox (badness 10000) in paragraph at lines 7084--7096

 []


Underfull \hbox (badness 10000) in paragraph at lines 7084--7096

 []


Underfull \hbox (badness 10000) in paragraph at lines 7084--7096

 []


Underfull \hbox (badness 10000) in paragraph at lines 7097--7109

 []


Underfull \hbox (badness 10000) in paragraph at lines 7097--7109

 []


Underfull \hbox (badness 10000) in paragraph at lines 7097--7109

 []


Underfull \hbox (badness 10000) in paragraph at lines 7097--7109

 []


Underfull \hbox (badness 10000) in paragraph at lines 7097--7109

 []


Underfull \hbox (badness 10000) in paragraph at lines 7097--7109

 []

[177]
File: Figures/msd_input_file.eps Graphic file (type eps)
 <Figures/msd_input_file.eps> [178] [179

] [180] [181]
Appendix A.
[182

] [183] (./nMOLDYN_for_HTML.aux)

LaTeX Font Warning: Some font shapes were not available, defaults substituted.


LaTeX Warning: There were multiply-defined labels.

 ) 
Here is how much of TeX's memory you used:
 2318 strings out of 95847
 29339 string characters out of 1195963
 125747 words of memory out of 1000001
 5171 multiletter control sequences out of 10000+50000
 13484 words of font info for 47 fonts, out of 500000 for 1000
 14 hyphenation exceptions out of 1000
 25i,12n,22p,306b,449s stack positions out of 1500i,500n,5000p,200000b,5000s

Output written on nMOLDYN_for_HTML.dvi (185 pages, 544292 bytes).
