diff --git a/doc/main.aux b/doc/main.aux new file mode 100644 index 0000000..aba7e1c --- /dev/null +++ b/doc/main.aux @@ -0,0 +1,14 @@ +\relax +\providecommand\hyper@newdestlabel[2]{} +\providecommand\HyField@AuxAddToFields[1]{} +\providecommand\HyField@AuxAddToCoFields[2]{} +\@writefile{toc}{\contentsline {section}{\numberline {1}Wprowadzenie}{1}{section.1}\protected@file@percent } +\@writefile{toc}{\contentsline {section}{\numberline {2}Opis dziaÅ‚ania narzÄ™dzia}{1}{section.2}\protected@file@percent } +\@writefile{toc}{\contentsline {section}{\numberline {3}PrzykÅ‚ad zastosowania}{2}{section.3}\protected@file@percent } +\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces Parametry symulacji}}{2}{table.1}\protected@file@percent } +\newlabel{tab:parametry}{{1}{2}{Parametry symulacji}{table.1}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Zmiana energii potencjalnej ukÅ‚adu w czasie symulacji.}}{2}{figure.1}\protected@file@percent } +\newlabel{rys:wyniki}{{1}{2}{Zmiana energii potencjalnej ukÅ‚adu w czasie symulacji}{figure.1}{}} +\@writefile{toc}{\contentsline {section}{\numberline {4}Analiza wyników}{2}{section.4}\protected@file@percent } +\@writefile{toc}{\contentsline {section}{\numberline {5}Wnioski}{3}{section.5}\protected@file@percent } +\gdef \@abspage@last{3} diff --git a/doc/main.log b/doc/main.log new file mode 100644 index 0000000..4ee7320 --- /dev/null +++ b/doc/main.log @@ -0,0 +1,448 @@ +This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex 2024.12.27) 16 APR 2025 18:17 +entering extended mode + restricted \write18 enabled. + %&-line parsing enabled. +**main +(./main.tex +LaTeX2e <2024-11-01> +L3 programming layer <2024-11-02> +(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls +Document Class: article 2024/06/29 v1.4n Standard LaTeX document class +(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo +File: size12.clo 2024/06/29 v1.4n Standard LaTeX file (size option) +) +\c@part=\count196 +\c@section=\count197 +\c@subsection=\count198 +\c@subsubsection=\count199 +\c@paragraph=\count266 +\c@subparagraph=\count267 +\c@figure=\count268 +\c@table=\count269 +\abovecaptionskip=\skip49 +\belowcaptionskip=\skip50 +\bibindent=\dimen141 +) +(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty +Package: inputenc 2024/02/08 v1.3d Input encoding file +\inpenc@prehook=\toks17 +\inpenc@posthook=\toks18 +) +(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty +Package: fontenc 2021/04/29 v2.0v Standard LaTeX package +) +(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty +Package: graphicx 2021/09/16 v1.2d Enhanced LaTeX Graphics (DPC,SPQR) + +(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty +Package: keyval 2022/05/29 v1.15 key=value parser (DPC) +\KV@toks@=\toks19 +) +(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty +Package: graphics 2024/08/06 v1.4g Standard LaTeX Graphics (DPC,SPQR) + +(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty +Package: trig 2023/12/02 v1.11 sin cos tan (DPC) +) +(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg +File: graphics.cfg 2016/06/04 v1.11 sample graphics configuration +) +Package graphics Info: Driver file: pdftex.def on input line 106. + +(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def +File: pdftex.def 2024/04/13 v1.2c Graphics/color driver for pdftex +)) +\Gin@req@height=\dimen142 +\Gin@req@width=\dimen143 +) +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty +Package: hyperref 2024-11-05 v7.01l Hypertext links for LaTeX + +(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty +Package: iftex 2022/02/03 v1.0f TeX engine tests +) +(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty +Package: kvsetkeys 2022-10-05 v1.19 Key value parser (HO) +) +(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty +Package: kvdefinekeys 2019-12-19 v1.6 Define keys (HO) +) +(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty +Package: pdfescape 2019/12/09 v1.15 Implements pdfTeX's escape features (HO) + +(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty +Package: ltxcmds 2023-12-04 v1.26 LaTeX kernel commands for general use (HO) +) +(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty +Package: pdftexcmds 2020-06-27 v0.33 Utility functions of pdfTeX for LuaTeX (HO +) + +(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty +Package: infwarerr 2019/12/03 v1.5 Providing info/warning/error messages (HO) +) +Package pdftexcmds Info: \pdf@primitive is available. +Package pdftexcmds Info: \pdf@ifprimitive is available. +Package pdftexcmds Info: \pdfdraftmode found. +)) +(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty +Package: hycolor 2020-01-27 v1.10 Color options for hyperref/bookmark (HO) +) +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty +Package: nameref 2023-11-26 v2.56 Cross-referencing by name of section + +(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty +Package: refcount 2019/12/15 v3.6 Data extraction from label references (HO) +) +(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty +Package: gettitlestring 2019/12/15 v1.6 Cleanup title references (HO) + +(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty +Package: kvoptions 2022-06-15 v3.15 Key value format for package options (HO) +)) +\c@section@level=\count270 +) +(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty +Package: etoolbox 2020/10/05 v2.5k e-TeX tools for LaTeX (JAW) +\etb@tempcnta=\count271 +) +(/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty +Package: stringenc 2019/11/29 v1.12 Convert strings between diff. encodings (HO +) +) +\@linkdim=\dimen144 +\Hy@linkcounter=\count272 +\Hy@pagecounter=\count273 + +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def +File: pd1enc.def 2024-11-05 v7.01l Hyperref: PDFDocEncoding definition (HO) +Now handling font encoding PD1 ... +... no UTF-8 mapping file for font encoding PD1 +) +(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty +Package: intcalc 2019/12/15 v1.3 Expandable calculations with integers (HO) +) +\Hy@SavedSpaceFactor=\count274 + +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def +File: puenc.def 2024-11-05 v7.01l Hyperref: PDF Unicode definition (HO) +Now handling font encoding PU ... +... no UTF-8 mapping file for font encoding PU +) +Package hyperref Info: Hyper figures OFF on input line 4157. +Package hyperref Info: Link nesting OFF on input line 4162. +Package hyperref Info: Hyper index ON on input line 4165. +Package hyperref Info: Plain pages OFF on input line 4172. +Package hyperref Info: Backreferencing OFF on input line 4177. +Package hyperref Info: Implicit mode ON; LaTeX internals redefined. +Package hyperref Info: Bookmarks ON on input line 4424. +\c@Hy@tempcnt=\count275 + +(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty +\Urlmuskip=\muskip17 +Package: url 2013/09/16 ver 3.4 Verb mode for urls, etc. +) +LaTeX Info: Redefining \url on input line 4763. +\XeTeXLinkMargin=\dimen145 + +(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty +Package: bitset 2019/12/09 v1.3 Handle bit-vector datatype (HO) + +(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty +Package: bigintcalc 2019/12/15 v1.5 Expandable calculations on big integers (HO +) +)) +\Fld@menulength=\count276 +\Field@Width=\dimen146 +\Fld@charsize=\dimen147 +Package hyperref Info: Hyper figures OFF on input line 6042. +Package hyperref Info: Link nesting OFF on input line 6047. +Package hyperref Info: Hyper index ON on input line 6050. +Package hyperref Info: backreferencing OFF on input line 6057. +Package hyperref Info: Link coloring OFF on input line 6062. +Package hyperref Info: Link coloring with OCG OFF on input line 6067. +Package hyperref Info: PDF/A mode OFF on input line 6072. + +(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty +Package: atbegshi-ltx 2021/01/10 v1.0c Emulation of the original atbegshi +package with kernel methods +) +\Hy@abspage=\count277 +\c@Item=\count278 +\c@Hfootnote=\count279 +) +Package hyperref Info: Driver (autodetected): hpdftex. + +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def +File: hpdftex.def 2024-11-05 v7.01l Hyperref driver for pdfTeX + +(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty +Package: atveryend-ltx 2020/08/19 v1.0a Emulation of the original atveryend pac +kage +with kernel methods +) +\Fld@listcount=\count280 +\c@bookmark@seq@number=\count281 + +(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty +Package: rerunfilecheck 2022-07-10 v1.10 Rerun checks for auxiliary files (HO) + +(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty +Package: uniquecounter 2019/12/15 v1.4 Provide unlimited unique counter (HO) +) +Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2 +85. +) +\Hy@SectionHShift=\skip51 +) +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty +Package: amsmath 2024/11/05 v2.17t AMS math features +\@mathmargin=\skip52 + +For additional information on amsmath, use the `?' option. +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty +Package: amstext 2021/08/26 v2.01 AMS text + +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty +File: amsgen.sty 1999/11/30 v2.0 generic functions +\@emptytoks=\toks20 +\ex@=\dimen148 +)) +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty +Package: amsbsy 1999/11/29 v1.2d Bold Symbols +\pmbraise@=\dimen149 +) +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty +Package: amsopn 2022/04/08 v2.04 operator names +) +\inf@bad=\count282 +LaTeX Info: Redefining \frac on input line 233. +\uproot@=\count283 +\leftroot@=\count284 +LaTeX Info: Redefining \overline on input line 398. +LaTeX Info: Redefining \colon on input line 409. +\classnum@=\count285 +\DOTSCASE@=\count286 +LaTeX Info: Redefining \ldots on input line 495. +LaTeX Info: Redefining \dots on input line 498. +LaTeX Info: Redefining \cdots on input line 619. +\Mathstrutbox@=\box52 +\strutbox@=\box53 +LaTeX Info: Redefining \big on input line 721. +LaTeX Info: Redefining \Big on input line 722. +LaTeX Info: Redefining \bigg on input line 723. +LaTeX Info: Redefining \Bigg on input line 724. +\big@size=\dimen150 +LaTeX Font Info: Redeclaring font encoding OML on input line 742. +LaTeX Font Info: Redeclaring font encoding OMS on input line 743. +\macc@depth=\count287 +LaTeX Info: Redefining \bmod on input line 904. +LaTeX Info: Redefining \pmod on input line 909. +LaTeX Info: Redefining \smash on input line 939. +LaTeX Info: Redefining \relbar on input line 969. +LaTeX Info: Redefining \Relbar on input line 970. +\c@MaxMatrixCols=\count288 +\dotsspace@=\muskip18 +\c@parentequation=\count289 +\dspbrk@lvl=\count290 +\tag@help=\toks21 +\row@=\count291 +\column@=\count292 +\maxfields@=\count293 +\andhelp@=\toks22 +\eqnshift@=\dimen151 +\alignsep@=\dimen152 +\tagshift@=\dimen153 +\tagwidth@=\dimen154 +\totwidth@=\dimen155 +\lineht@=\dimen156 +\@envbody=\toks23 +\multlinegap=\skip53 +\multlinetaggap=\skip54 +\mathdisplay@stack=\toks24 +LaTeX Info: Redefining \[ on input line 2953. +LaTeX Info: Redefining \] on input line 2954. +) +(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty +Package: geometry 2020/01/02 v5.9 Page Geometry + +(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty +Package: ifvtex 2019/10/25 v1.7 ifvtex legacy package. Use iftex instead. +) +\Gm@cnth=\count294 +\Gm@cntv=\count295 +\c@Gm@tempcnt=\count296 +\Gm@bindingoffset=\dimen157 +\Gm@wd@mp=\dimen158 +\Gm@odd@mp=\dimen159 +\Gm@even@mp=\dimen160 +\Gm@layoutwidth=\dimen161 +\Gm@layoutheight=\dimen162 +\Gm@layouthoffset=\dimen163 +\Gm@layoutvoffset=\dimen164 +\Gm@dimlist=\toks25 +) +(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def +File: l3backend-pdftex.def 2024-05-08 L3 backend support: PDF output (pdfTeX) +\l__color_backend_stack_int=\count297 +\l__pdf_internal_box=\box54 +) +No file main.aux. +\openout1 = `main.aux'. + +LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 14. +LaTeX Font Info: ... okay on input line 14. +LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 14. +LaTeX Font Info: ... okay on input line 14. +LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 14. +LaTeX Font Info: ... okay on input line 14. +LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 14. +LaTeX Font Info: ... okay on input line 14. +LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 14. +LaTeX Font Info: ... okay on input line 14. +LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 14. +LaTeX Font Info: ... okay on input line 14. +LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 14. +LaTeX Font Info: ... okay on input line 14. +LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 14. +LaTeX Font Info: ... okay on input line 14. +LaTeX Font Info: Checking defaults for PU/pdf/m/n on input line 14. +LaTeX Font Info: ... okay on input line 14. +(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii +[Loading MPS to PDF converter (version 2006.09.02).] +\scratchcounter=\count298 +\scratchdimen=\dimen165 +\scratchbox=\box55 +\nofMPsegments=\count299 +\nofMParguments=\count300 +\everyMPshowfont=\toks26 +\MPscratchCnt=\count301 +\MPscratchDim=\dimen166 +\MPnumerator=\count302 +\makeMPintoPDFobject=\count303 +\everyMPtoPDFconversion=\toks27 +) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty +Package: epstopdf-base 2020-01-24 v2.11 Base part for package epstopdf +Package epstopdf-base Info: Redefining graphics rule for `.eps' on input line 4 +85. + +(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg +File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Liv +e +)) +Package hyperref Info: Link coloring OFF on input line 14. +\@outlinefile=\write3 +\openout3 = `main.out'. + + +*geometry* driver: auto-detecting +*geometry* detected driver: pdftex +*geometry* verbose mode - [ preamble ] result: +* driver: pdftex +* paper: a4paper +* layout: +* layoutoffset:(h,v)=(0.0pt,0.0pt) +* modes: +* h-part:(L,W,R)=(72.26999pt, 452.9679pt, 72.26999pt) +* v-part:(T,H,B)=(72.26999pt, 700.50687pt, 72.26999pt) +* \paperwidth=597.50787pt +* \paperheight=845.04684pt +* \textwidth=452.9679pt +* \textheight=700.50687pt +* \oddsidemargin=0.0pt +* \evensidemargin=0.0pt +* \topmargin=-37.0pt +* \headheight=12.0pt +* \headsep=25.0pt +* \topskip=12.0pt +* \footskip=30.0pt +* \marginparwidth=35.0pt +* \marginparsep=10.0pt +* \columnsep=10.0pt +* \skip\footins=10.8pt plus 4.0pt minus 2.0pt +* \hoffset=0.0pt +* \voffset=0.0pt +* \mag=1000 +* \@twocolumnfalse +* \@twosidefalse +* \@mparswitchfalse +* \@reversemarginfalse +* (1in=72.27pt=25.4mm, 1cm=28.453pt) + + +Overfull \hbox (0.3298pt too wide) in paragraph at lines 36--37 +\T1/cmr/m/n/12 prowad-zone w okre±lonych warunk-ach ter-mo-dy-nam-icznych (np. +staªa tem-per-atura, ci±nie- + [] + + +LaTeX Warning: Reference `tab:parametry' on page 1 undefined on input line 47. + + + +[1 + +{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texmf/fonts/enc/ +dvips/cm-super/cm-super-t1.enc}] + +LaTeX Warning: Reference `rys:wyniki' on page 2 undefined on input line 66. + + +LaTeX Warning: File `energia.png' not found on input line 70. + + +! Package pdftex.def Error: File `energia.png' not found: using draft setting. + +See the pdftex.def package documentation for explanation. +Type H for immediate help. + ... + +l.70 ...graphics[width=0.8\textwidth]{energia.png} + +? + + +[2] + +[3] (./main.aux) + *********** +LaTeX2e <2024-11-01> +L3 programming layer <2024-11-02> + *********** + + +LaTeX Warning: There were undefined references. + + +LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. + + +Package rerunfilecheck Warning: File `main.out' has changed. +(rerunfilecheck) Rerun to get outlines right +(rerunfilecheck) or use package `bookmark'. + +Package rerunfilecheck Info: Checksums for `main.out': +(rerunfilecheck) Before: +(rerunfilecheck) After: 739E533CAAC60275D26BA3AC45746822;634. + ) +Here is how much of TeX's memory you used: + 9902 strings out of 473362 + 150710 string characters out of 5723554 + 560922 words of memory out of 5000000 + 32896 multiletter control sequences out of 15000+600000 + 570795 words of font info for 64 fonts, out of 8000000 for 9000 + 1141 hyphenation exceptions out of 8191 + 75i,8n,79p,510b,465s stack positions out of 10000i,1000n,20000p,200000b,200000s + + +Output written on main.pdf (3 pages, 176148 bytes). +PDF statistics: + 82 PDF objects out of 1000 (max. 8388607) + 58 compressed objects within 1 object stream + 16 named destinations out of 1000 (max. 500000) + 1 words of extra memory for PDF output out of 10000 (max. 10000000) + diff --git a/doc/main.out b/doc/main.out new file mode 100644 index 0000000..b2c67ad --- /dev/null +++ b/doc/main.out @@ -0,0 +1,5 @@ +\BOOKMARK [1][-]{section.1}{\376\377\000W\000p\000r\000o\000w\000a\000d\000z\000e\000n\000i\000e}{}% 1 +\BOOKMARK [1][-]{section.2}{\376\377\000O\000p\000i\000s\000\040\000d\000z\000i\000a\001\102\000a\000n\000i\000a\000\040\000n\000a\000r\000z\001\031\000d\000z\000i\000a}{}% 2 +\BOOKMARK [1][-]{section.3}{\376\377\000P\000r\000z\000y\000k\001\102\000a\000d\000\040\000z\000a\000s\000t\000o\000s\000o\000w\000a\000n\000i\000a}{}% 3 +\BOOKMARK [1][-]{section.4}{\376\377\000A\000n\000a\000l\000i\000z\000a\000\040\000w\000y\000n\000i\000k\000\363\000w}{}% 4 +\BOOKMARK [1][-]{section.5}{\376\377\000W\000n\000i\000o\000s\000k\000i}{}% 5 diff --git a/doc/main.pdf b/doc/main.pdf new file mode 100644 index 0000000..65e700e Binary files /dev/null and b/doc/main.pdf differ diff --git a/doc/main.tex b/doc/main.tex new file mode 100644 index 0000000..f7919e4 --- /dev/null +++ b/doc/main.tex @@ -0,0 +1,89 @@ +\documentclass[12pt,a4paper]{article} +\usepackage[utf8]{inputenc} +\usepackage[T1]{fontenc} +\usepackage{graphicx} +\usepackage{hyperref} +\usepackage{amsmath} +\usepackage{geometry} +\geometry{a4paper, margin=1in} + +\title{\textbf{Raport dotyczÄ…cy narzÄ™dzia NAMD}} +\author{ImiÄ™ Nazwisko \\ Grupa/Instytucja \\ Data: \today} +\date{} + +\begin{document} + +\maketitle + +\begin{abstract} +NAMD (Not Another Molecular Dynamics Program) to zaawansowane narzÄ™dzie do symulacji dynamiki molekularnej, które umożliwia badanie zachowania ukÅ‚adów biologicznych na poziomie atomowym. Niniejszy raport przedstawia podstawowe informacje o narzÄ™dziu, jego zastosowaniach oraz analizÄ™ wyników uzyskanych w ramach przeprowadzonych symulacji. Celem pracy jest zaprezentowanie możliwoÅ›ci NAMD i omówienie jego roli w badaniach naukowych. +\end{abstract} + +\section{Wprowadzenie} +NAMD jest narzÄ™dziem typu open-source przeznaczonym do wykonywania symulacji dynamiki molekularnej (MD). NarzÄ™dzie to jest szczególnie popularne w dziedzinie biofizyki i chemii obliczeniowej, gdzie sÅ‚uży do badania struktury i funkcji biaÅ‚ek, lipidów, kwasów nukleinowych oraz innych ukÅ‚adów biologicznych. DziÄ™ki zoptymalizowanemu algorytmowi równolegÅ‚ego przetwarzania danych, NAMD umożliwia wydajne przeprowadzanie symulacji nawet dla dużych ukÅ‚adów molekularnych. + +Główne cechy NAMD to: + + +- Skalowalność na systemach wieloprocesorowych, + +- Kompatybilność z formatami plików CHARMM i AMBER, + +- ObsÅ‚uga zaawansowanych modeli fizycznych, takich jak siÅ‚y van der Waalsa czy oddziaÅ‚ywania elektrostatyczne. + + +\section{Opis dziaÅ‚ania narzÄ™dzia} +NAMD dziaÅ‚a w oparciu o metodÄ™ dynamiki molekularnej, która polega na numerycznym rozwiÄ…zywaniu równaÅ„ ruchu Newtona dla każdego atomu w ukÅ‚adzie. Symulacje sÄ… prowadzone w okreÅ›lonych warunkach termodynamicznych (np. staÅ‚a temperatura, ciÅ›nienie), co pozwala na analizÄ™ zachowania ukÅ‚adu w różnych Å›rodowiskach. + +Podstawowe etapy pracy z NAMD obejmujÄ…: +\begin{enumerate} + \item Przygotowanie plików wejÅ›ciowych, w tym pliku topologii (\texttt{.psf}) i współrzÄ™dnych poczÄ…tkowych (\texttt{.pdb}), + \item KonfiguracjÄ™ parametrów symulacji w pliku kontrolnym (\texttt{.conf}), + \item Uruchomienie symulacji na klastrze komputerowym lub lokalnym serwerze, + \item AnalizÄ™ wyników za pomocÄ… narzÄ™dzi wizualizacyjnych, takich jak VMD (Visual Molecular Dynamics). +\end{enumerate} + +\section{PrzykÅ‚ad zastosowania} +W ramach badaÅ„ przeprowadzono symulacjÄ™ ukÅ‚adu biaÅ‚kowego w Å›rodowisku wodnym. W tabeli~\ref{tab:parametry} przedstawiono kluczowe parametry użyte w symulacji. + +\begin{table}[h!] +\centering +\caption{Parametry symulacji} +\label{tab:parametry} +\begin{tabular}{|l|c|} +\hline +\textbf{Parametr} & \textbf{Wartość} \\ +\hline +Czas symulacji & 50 ns \\ +Krok czasowy & 2 fs \\ +Temperatura & 300 K \\ +CiÅ›nienie & 1 atm \\ +Metoda integracji & Verlet \\ +\hline +\end{tabular} +\end{table} + +Na rysunku~\ref{rys:wyniki} przedstawiono zmianÄ™ energii potencjalnej ukÅ‚adu w funkcji czasu. + +\begin{figure}[h!] +\centering +\includegraphics[width=0.8\textwidth]{energia.png} +\caption{Zmiana energii potencjalnej ukÅ‚adu w czasie symulacji.} +\label{rys:wyniki} +\end{figure} + +\section{Analiza wyników} +Symulacja wykazaÅ‚a stabilność ukÅ‚adu w okreÅ›lonych warunkach termodynamicznych. Energia potencjalna ukÅ‚adu osiÄ…gnęła plateau po okoÅ‚o 10 ns, co sugeruje, że ukÅ‚ad osiÄ…gnÄ…Å‚ równowagÄ™. Dodatkowo analiza trajektorii wykazaÅ‚a, że struktura biaÅ‚ka pozostaÅ‚a niezmieniona w trakcie symulacji, co potwierdza poprawność przyjÄ™tych parametrów. + +\section{Wnioski} +NAMD okazaÅ‚ siÄ™ być potężnym narzÄ™dziem do symulacji dynamiki molekularnej, oferujÄ…c zarówno wysokÄ… wydajność, jak i elastyczność w konfiguracji. NarzÄ™dzie to jest szczególnie przydatne w badaniach ukÅ‚adów biologicznych, gdzie precyzja i skalowalność sÄ… kluczowe. Wyniki przeprowadzonych symulacji potwierdzajÄ… stabilność badanego ukÅ‚adu i mogÄ… stanowić podstawÄ™ do dalszych badaÅ„ nad interakcjami molekularnymi. + +\section*{Bibliografia} + + +- Phillips, J. C., et al. "Scalable molecular dynamics with NAMD." \textit{Journal of Computational Chemistry}, 2005. + +- Humphrey, W., Dalke, A., Schulten, K. "VMD - Visual Molecular Dynamics." \textit{Journal of Molecular Graphics}, 1996. + + +\end{document} \ No newline at end of file