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517 lines
17 KiB
TeX
517 lines
17 KiB
TeX
%
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% $Id$
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%
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\label{sec:formats}
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\section {Format fragment file}
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\begin{table}[h]
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\begin{center}
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\begin{tabular}{p{15mm}p{12mm}l}
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\hline\hline
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Card & Format & Description \\ \hline
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I-1-1 & a1 & \$ or \# comments to describe fragment \\ % $ for emacs
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\hline
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I-2-1 & i5 & number of atoms in the fragment\\
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I-2-2 & i5 & number of parameter sets\\
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I-2-3 & i5 & default parameter set\\
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I-2-4 & i5 & number of z-matrix definition\\
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\hline
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\mc{3}{l}{For each parameter set one card I-3} \\
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\hline
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I-3-1 & a & residue name for parameter set\\
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\hline
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\mc{3}{l}{For each atom one deck II} \\
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\hline
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II-1-1 & i5 & atom sequence number \\
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II-1-2 & a6 & atom name \\
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II-1-3 & a5 & atom type \\
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II-1-4 & a1 & dynamics type\\
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& & \verb+ + : normal\\
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& & \verb+D+ : dummy atom\\
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& & \verb+S+ : solute interactions only\\
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& & \verb+Q+ : quantum atom\\
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& & other : intramolecular solute interactions only\\
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II-1-5 & i5 & link number\\
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& & 0: no link\\
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& & 1: first atom in chain\\
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& & 2: second atom in chain\\
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& & 3 and up: other links\\
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II-1-6 & i5 & environment type\\
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& & 0: no special identifier\\
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& & 1: planar, using improper torsion\\
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& & 2: tetrahedral, using improper torsion\\
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& & 3: tetrahedral, using improper torsion\\
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& & 4: atom in aromatic ring\\
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II-1-7 & i5 & \\
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II-1-8 & i5 & charge group\\
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II-1-9 & i5 & polarization group\\
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II-1-10 & f12.6 & atomic partial charge\\
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II-1-11 & f12.6 & atomic polarizability\\
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\hline
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For each additional parameter set on card II-2\\
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\hline
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II-2-1 & 11x,a6 & atom type\\
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II-2-2 & a1 & dynamics type\\
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& & \verb+ + : normal\\
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& & \verb+D+ : dummy atom\\
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& & \verb+S+ : solute interactions only\\
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& & \verb+Q+ : quantum atom\\
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& & other : intramolecular solute interactions only\\
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II-2-7 & 25x,f12.6 & atomic partial charge\\
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II-2-8 & f12.6 & atomic polarizability\\
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\hline
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\mc{3}{l}{Any number of cards in deck III to specify complete
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connectivity} \\
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\hline
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III-1-1 & 16i5 & connectivity, duplication allowed\\
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\hline
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One blank card to signal the end of the connectivity list\\
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\hline
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For each z-matrix definition one card IV\\
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\hline
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IV-1-1 & i5 & atom i \\
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IV-1-2 & i5 & atom j \\
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IV-1-3 & i5 & atom k \\
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IV-1-4 & i5 & atom l \\
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IV-1-5 & f12.6 & bond length i-j\\
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IV-1-6 & f12.6 & angle i-j-k\\
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IV-1-7 & f12.6 & torson i-j-k-l\\
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\hline\hline
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\end{tabular}
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\caption{The format of fragment files.\label{tbl:nwmdfrg}}
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\end{center}
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\end{table}
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\section {Format segment file}
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\begin{table}[h]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Deck & Format & Description \\ \hline
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I-0-1 & & \# lines at top are comments \\
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I-1-1 & a1 & \$ to identify the start of a segment \\ %$ for emacs
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I-1-2 & a10 & name of the segment, the tenth character\\
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& & N: identifies beginning of a chain\\
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& & C: identifies end of a chain\\
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& & blank: identifies chain fragment\\
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& & M: identifies an integral molecule\\
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\hline
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I-2-1 & f12.6 & version number \\
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\hline
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I-3-1 & i5 & number of atoms in the segment\\
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I-3-2 & i5 & number of bonds in the segment\\
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I-3-3 & i5 & number of angles in the segment\\
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I-3-4 & i5 & number of proper dihedrals in the segment\\
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I-3-5 & i5 & number of improper dihedrals in the segment\\
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I-3-6 & i5 & number of z-matrix definitions\\
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I-3-7 & i5 & number of parameter sets \\
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1-3-8 & i5 & default parameter set\\
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\hline
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For each prarmeter set one card I-4\\
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\hline
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I-4-1 & f12.6 & dipole correction energy \\
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\hline
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\end{tabular*}
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\caption{Segment file format, table 1 of 7.\label{tbl:nwmdseg1}}
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\end{center}
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\end{table}
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\begin{table}[h]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Deck & Format & Description \\ \hline
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\mc{3}{l}{For each atom one deck II} \\
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\hline
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II-1-1 & i5 & atom sequence number \\
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II-1-2 & a6 & atom name \\
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II-1-3 & i5 & link number\\
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II-1-4 & i5 & environment type\\
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& & 0: no special identifier\\
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& & 1: planar, using improper torsion\\
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& & 2: tetrahedral, using improper torsion\\
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& & 3: tetrahedral, using improper torsion\\
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& & 4: atom in aromatic ring\\
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II-1-5 & i5 & \\
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II-1-6 & i5 & charge group\\
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II-1-7 & i5 & polarization group\\
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\hline
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For each parameter set one card II-2\\
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\hline
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II-2-1 & 5x,a5 & atom type \\
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II-2-2 & a1 & dynamics type\\
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& & \verb+ + : normal\\
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& & \verb+D+ : dummy atom\\
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& & \verb+S+ : solute interactions only\\
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& & \verb+Q+ : quantum atom\\
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& & other : intramolecular solute interactions only\\
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II-2-3 & f12.6 & atomic partial charge in e\\
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II-2-4 & f12.6 & atomic polarizability/$4\pi\epsilon_o$ in nm$^3$\\
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\hline
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\end{tabular*}
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\caption{Segment file format, table 2 of 7.\label{tbl:nwmdseg2}}
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\end{center}
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\end{table}
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\begin{table}[h]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Deck & Format & Description \\ \hline
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\mc{3}{l}{For each bond a deck III} \\
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III-1-1 & i5 & bond sequence number \\
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III-1-2 & i5 & bond atom i \\
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III-1-3 & i5 & bond atom j \\
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III-1-4 & i5 & bond type \\
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& & 0: harmonic\\
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& & 1: constrained bond\\
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III-1-5 & i5 & bond parameter origin\\
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& & 0: from database, next card ignored \\
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& & 1: from next card\\
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\hline
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For each parameter set one card III-2\\
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\hline
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III-2-1 & f12.6 & bond length in nm\\
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III-2-2 & e12.5 & bond force constant in kJ nm$^2$ mol$^{-1}$\\
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\hline
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\end{tabular*}
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\caption{Segment file format, table 3 of 7.\label{tbl:nwmdseg3}}
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\end{center}
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\end{table}
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\begin{table}
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Deck & Format & Description \\ \hline
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\mc{3}{l}{For each angle a deck IV} \\
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IV-1-1 & i5 & angle sequence number \\
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IV-1-2 & i5 & angle atom i \\
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IV-1-3 & i5 & angle atom j \\
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IV-1-4 & i5 & angle atom k \\
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IV-1-5 & i5 & angle type \\
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& & 0: harmonic\\
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IV-1-6 & i5 & angle parameter origin\\
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& & 0: from database, next card ignored \\
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& & 1: from next card\\
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\hline
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For each parameter set one card IV-2\\
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\hline
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IV-2-1 & f10.6 & angle in radians\\
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IV-2-2 & e12.5 & angle force constant in kJ mol$^{-1}$\\
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\hline
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\end{tabular*}
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\caption{Segment file format, table 4 of 7.\label{tbl:nwmdseg4}}
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\end{center}
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\end{table}
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\begin{table}[h]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Deck & Format & Description \\ \hline
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\mc{3}{l}{For each proper dihedral a deck V} \\
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V-1-1 & i5 & proper dihedral sequence number \\
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V-1-2 & i5 & proper dihedral atom i \\
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V-1-3 & i5 & proper dihedral atom j \\
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V-1-4 & i5 & proper dihedral atom k \\
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V-1-5 & i5 & proper dihedral atom l \\
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V-1-6 & i5 & proper dihedral type \\
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& & 0: $C\cos(m\phi-\delta)$\\
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V-1-7 & i5 & proper dihedral parameter origin\\
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& & 0: from database, next card ignored \\
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& & 1: from next card\\
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\hline
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For each parameter set one card V-2\\
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\hline
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V-2-1 & i3 & multiplicity\\
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V-2-2 & f10.6 & proper dihedral in radians\\
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V-2-3 & e12.5 & proper dihedral force constant in kJ mol$^{-1}$\\
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\hline
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\end{tabular*}
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\caption{Segment file format, table 5 of 7.\label{tbl:nwmdseg5}}
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\end{center}
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\end{table}
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\begin{table}[h]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Deck & Format & Description \\ \hline
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\mc{3}{l}{For each improper dihedral a deck VI} \\
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VI-1-1 & i5 & improper dihedral sequence number \\
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VI-1-2 & i5 & improper dihedral atom i \\
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VI-1-3 & i5 & improper dihedral atom j \\
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VI-1-4 & i5 & improper dihedral atom k \\
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VI-1-5 & i5 & improper dihedral atom l \\
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VI-1-6 & i5 & improper dihedral type \\
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& & 0: harmonic\\
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VI-1-7 & i5 & improper dihedral parameter origin\\
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& & 0: from database, next card ignored \\
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& & 1: from next card\\
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\hline
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For each parameter set one card VI-2\\
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\hline
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VI-2-1 & 3x,f10.6 & improper dihedral in radians\\
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VI-2-2 & e12.5 & improper dihedral force constant in kJ mol$^{-1}$\\
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\hline\hline
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\end{tabular*}
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\caption{Segment file format, table 6 of 7.\label{tbl:nwmdseg6}}
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\end{center}
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\end{table}
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\begin{table}[h]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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For each z-matrix definition one card VII\\
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\hline
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VII-1-1 & i5 & atom i \\
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VII-1-2 & i5 & atom j \\
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VII-1-3 & i5 & atom k \\
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VII-1-4 & i5 & atom l \\
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VII-1-5 & f12.6 & bond length i-j\\
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VII-1-6 & f12.6 & angle i-j-k\\
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VII-1-7 & f12.6 & torson i-j-k-l\\
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\hline\hline
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\end{tabular*}
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\caption{Segment file format, table 6 of 7.\label{tbl:nwmdseg7}}
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\end{center}
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\end{table}
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\section {Format sequence file}
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\begin{table}[h]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Card & Format & Description \\ \hline
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I-1-1 & a1 & \$ to identify the start of a sequence \\ %$ for emacs
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I-1-2 & a10 & name of the sequence\\
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\hline
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\mc{3}{l}{Any number of cards 1 and 2 in deck II to specify the system} \\
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\hline
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II-1-1 & i5 & segment number\\
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II-1-2 & a10 & segment name, last character will be determined from chain\\
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\hline
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II-2-1 & a & \verb+break+ to identify a break in the molecule chain\\
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\hline
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II-2-1 & a & \verb+molecule+ to identify the end of a solute molecule\\
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\hline
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II-2-1 & a & \verb+fraction+ to identify the end of a solute fraction\\
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\hline
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II-2-1 & a5 & \verb+link + to specify a link\\
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II-2-2 & i5 & segment number of first link atom\\
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II-2-3 & a4 & name of first link atom \\
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II-2-4 & i5 & segment number of second link atom\\
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II-2-5 & a4 & name of second link atom \\
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\hline
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II-2-1 & a & \verb+solvent+ to identify solvent definition on next card\\
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\hline
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II-2-1 & a & \verb+stop+ to identify the end of the sequence\\
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\hline
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II-2-1 & a6 & \verb+repeat+ to repeat next $ncard$ cards $ncount$
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times\\
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II-2-2 & i5 & number of cards to repeat ($ncards$)\\
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II-2-3 & i5 & number of times to repeat cards ($ncount$)\\
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\mc{3}{l}{Any number of cards in deck II to specify the system} \\
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\hline\hline
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\end{tabular*}
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\caption{Sequence file format.\label{tbl:nwmdseq}}
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\end{center}
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\end{table}
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\section {Format trajectory file}
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\begin{table}[h]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Card & Format & Description \\ \hline
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I-1-1 & a6 & keyword \verb+header+ \\
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\hline
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I-2-1 & i10 & number of atoms per solvent molecule \\
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I-2-2 & i10 & number of solute atoms \\
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I-2-3 & i10 & number of solute bonds \\
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I-2-4 & i10 & number of solvent bonds \\
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I-2-5 & i10 & number of solvent molecules\\
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I-2-6 & i10 & precision of the coordinates. 0=standard, 1=high\\
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\hline
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\mc{3}{l}{For each atom per solvent molecule one card I-3} \\
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\hline
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I-3-1 & a5 & solvent name \\
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I-3-2 & a5 & atom name \\
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\hline
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\mc{3}{l}{For each solute atom one card I-4} \\
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\hline
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I-4-1 & a5 & segment name \\
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I-4-2 & a5 & atom name \\
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I-4-3 & i6 & segment number \\
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I-4-4 & i10 & solute atom counter \\
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I-4-5 & i5 & integer 1\\
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\hline
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\mc{3}{l}{For each solvent bond one card I-5} \\
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\hline
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I-5-1 & i8 & atom index i for bond between i and j \\
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I-5-2 & i8 & atom index j for bond between i and j \\
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\hline
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\mc{3}{l}{For each solute bond one card I-6} \\
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\hline
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I-6-1 & i8 & atom index i for bond between i and j \\
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I-6-2 & i8 & atom index j for bond between i and j \\
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\hline
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\mc{3}{l}{For each frame one deck II} \\
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\hline
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II-1-1 & a5 & keyword \verb+frame+ \\
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\hline
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II-2-1 & f12.6 & time of frame in ps \\
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II-2-2 & f12.6 & temperature of frame in K \\
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II-2-3 & e12.5 & pressure of frame in Pa \\
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II-2-4 & a10 & date \\
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II-2-5 & a10 & time \\
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\hline
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II-3-1 & f12.6 & box dimension x \\
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\hline
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II-3-2 & 12x,f12.6 & box dimension y \\
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\hline
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II-3-3 & 24x,f12.6 & box dimension z \\
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\hline
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II-4-1 & l1 & logical lxw for solvent coordinates \\
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II-4-2 & l1 & logical lvw for solvent velocities \\
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II-4-3 & l1 & logical lfw for solvent forces \\
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II-4-4 & l1 & logical lpw for solvent induced dipoles \\
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II-4-5 & l1 & logical lxs for solute coordinates \\
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II-4-6 & l1 & logical lvs for solute velocities \\
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II-4-7 & l1 & logical lfs for solute forces \\
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II-4-8 & l1 & logical lps for solute induced dipoles \\
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II-4-5 & i10 & number of solvent molecules \\
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II-4-6 & i10 & number of solvent atoms \\
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II-4-7 & i10 & number of solute atoms \\
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\hline\hline
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\end{tabular*}
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\caption{Trajectory file format.\label{tbl:nwmdtrj}}
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\end{center}
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\end{table}
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\begin{table}[h]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Card & Format & Description \\ \hline
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\mc{3}{l}{For each solvent molecule one card II-5 for each atom, if stardard precision} \\
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\hline
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II-5-1 & 3f8.3 & solvent atom coordinates, if lxw or lvw \\
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II-5-4 & 3f8.3 & solvent atom velocities, if lvw \\
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II-5-7 & 3f8.1 & solvent atom forces, if lfw\\
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\hline
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\mc{3}{l}{For each solute atom one card II-6 for each atom, if stardard precision} \\
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\hline
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II-6-1 & 3f8.3 & solute atom coordinates, if lxs or lvs \\
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II-6-4 & 3f8.3 & solute atom velocities, if lvs \\
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II-6-7 & 3f8.1 & solute atom forces, if lfs \\
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\hline
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\hline
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\mc{3}{l}{For each solvent molecule one card II-5 for each atom, if high precision} \\
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\hline
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II-5-1 & 3e12.6 & solvent atom coordinates, if lxw or lvw \\
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II-5-4 & 3e12.6 & solvent atom velocities, if lvw \\
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II-5-7 & 3e12.6 & solvent atom forces, if lfw (on new card if both lxw and lvw)\\
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\hline
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\mc{3}{l}{For each solute atom one card II-6 for each atom, if high precision} \\
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\hline
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II-6-1 & 3e12.6 & solute atom coordinates, if lxs or lvs \\
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II-6-4 & 3e12.6 & solute atom velocities, if lvs \\
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II-6-7 & 3e12.6 & solute atom forces, if lfs (on new card if both lxs and lvs)\\
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\hline\hline
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\end{tabular*}
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\caption{continued trajectory file format.\label{tbl:nwmdtrj2}}
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\end{center}
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\end{table}
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\section {Format free energy file}
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|
|
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\begin{table}[h]
|
|
\begin{center}
|
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
|
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\hline\hline
|
|
Card & Format & Description \\ \hline
|
|
\mc{3}{l}{For each step in $\lambda$ one deck I} \\
|
|
I-1-1 & i7 & number $nderiv$ of data summed in derivative decomposition array $deriv$ \\
|
|
I-1-2 & i7 & length $ndata$ of total derivative array $drf$ \\
|
|
I-1-3 & f12.6 & current value of $\lambda$ \\
|
|
I-1-4 & f12.6 & step size of $\lambda$ \\
|
|
\hline
|
|
I-2-1 & 4e12.12 & derivative decomposition array $deriv(1:24)$ \\
|
|
\hline
|
|
I-3-1 & 4e12.12 & total derivative array $dfr(1:nda)$ \\
|
|
\hline
|
|
I-4-1 & i10 & size of ensemble at current $\lambda$ \\
|
|
I-4-2 & e20.12 & average temperature at current $\lambda$ \\
|
|
I-4-3 & e20.12 & average exponent reverse perturbation energy at current $\lambda$ \\
|
|
I-4-4 & e20.12 & average exponent forward perturbation energy at current $\lambda$ \\
|
|
\hline\hline
|
|
\end{tabular*}
|
|
\caption{Free energy file format.\label{tbl:nwmdgib}}
|
|
\end{center}
|
|
\end{table}
|
|
|
|
\section {Format root mean square deviation file}
|
|
|
|
\begin{table}[h]
|
|
\begin{center}
|
|
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
|
|
\hline\hline
|
|
Card & Format & Description \\ \hline
|
|
\mc{3}{l}{For each analyzed time step one card I-1} \\
|
|
I-1-1 & f12.6 & time in ps \\
|
|
I-1-2 & f12.6 & total rms deviation of the selected atoms before superimposition \\
|
|
I-1-3 & f12.6 & total rms deviation of the selected atoms after superimposition \\
|
|
\hline
|
|
II-1-1 & a8 & keyword \verb+analysis+ \\
|
|
\hline
|
|
\mc{3}{l}{For each solute atom one card II-2} \\
|
|
\hline
|
|
II-2-1 & a5 & segment name \\
|
|
II-2-2 & a5 & atom name \\
|
|
II-2-3 & i6 & segment number \\
|
|
II-2-4 & i10 & atom number \\
|
|
II-2-5 & i5 & selected if 1 \\
|
|
II-2-6 & f12.6 & average atom rms deviation after superimposition \\
|
|
\hline
|
|
III-1-1 & a8 & keyword \verb+analysis+ \\
|
|
\hline
|
|
\mc{3}{l}{For each solute segment one card III-2} \\
|
|
III-2-1 & a5 & segment name \\
|
|
III-2-2 & i6 & segment number \\
|
|
III-2-3 & f12.6 & average segment rms deviation after superimposition \\
|
|
\hline\hline
|
|
\end{tabular*}
|
|
\caption{Root mean square deviation file format.\label{tbl:nwmdrms}}
|
|
\end{center}
|
|
\end{table}
|
|
|
|
\section {Format property file}
|
|
|
|
\begin{table}[h]
|
|
\begin{center}
|
|
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
|
|
\hline\hline
|
|
Card & Format & Description \\ \hline
|
|
I-1-1 & i7 & number $nprop$ of recorded properties \\
|
|
I-1-2 & 1x,2a10 & date and time \\
|
|
\hline
|
|
\mc{3}{l}{For each of the $nprop$ properties one card I-2} \\
|
|
\hline
|
|
I-2-1 & a50 & description of recorded property \\
|
|
\hline
|
|
\mc{3}{l}{For each recorded step one deck II} \\
|
|
\hline
|
|
II-1-1 & 4(1pe12.5) & value of property \\
|
|
\hline\hline
|
|
\end{tabular*}
|
|
\caption{Property file format.\label{tbl:nwmdprp}}
|
|
\end{center}
|
|
\end{table}
|
|
|