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34. File formats


Table 34.1: The format of fragment files.
Card Format Description
I-1-1 a1 $ to identify the start of a fragment
I-1-2 a10 name of the fragment, the tenth character
    N: identifies beginning of a chain
    C: identifies end of a chain
    blank: identifies chain fragment
    M: identifies an integral molecule
I-2-1 i5 number of atoms in the fragment
For each atom one deck II    
II-1-1 i5 atom sequence number
II-1-2 a6 atom name
II-1-3 a5 atom type
II-1-4 a1 dynamics type
    : normal
    D : dummy atom
    S : solute interactions only
    Q : quantum atom
    other : intramolecular solute interactions only
II-1-5 i5 link number
    0: no link
    1: first atom in chain
    2: second atom in chain
    3 and up: other links
II-1-6 i5 environment type
    0: no special identifier
    1: planar, using improper torsion
    2: tetrahedral, using improper torsion
    3: tetrahedral, using improper torsion
    4: atom in aromatic ring
II-1-7 i5 charge group
II-1-8 i5 polarization group
II-1-9 f12.6 atomic partial charge
II-1-10 f12.6 atomic polarizability
Any number of cards in deck III to specify complete connectivity    
III-1-1 16i5 connectivity, duplication allowed



Table 34.2: Segment file format, table 1 of 6.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...mproper dihedrals in the segment\\ \hline \end{tabular*}\end{center}\end{table}



Table 34.3: Segment file format, table 2 of 6.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...\pi\epsilon_o$\ in nm$^3$, set 3\\ \hline \end{tabular*}\end{center}\end{table}



Table 34.4: Segment file format, table 3 of 6.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...in kJ nm$^2$\ mol$^{-1}$, set 3 \\ \hline \end{tabular*}\end{center}\end{table}



Table 34.5: Segment file format, table 4 of 6.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...onstant in kJ mol$^{-1}$, set 3 \\ \hline \end{tabular*}\end{center}\end{table}



Table 34.6: Segment file format, table 5 of 6.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...onstant in kJ mol$^{-1}$, set 3 \\ \hline \end{tabular*}\end{center}\end{table}



Table 34.7: Segment file format, table 6 of 6.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...t in kJ mol$^{-1}$, set 3 \\ \hline\hline \end{tabular*}\end{center}\end{table}



Table 34.8: Sequence file format.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...II to specify the system} \\ \hline\hline \end{tabular*}\end{center}\end{table}



Table 34.9: Trajectory file format.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...e atom velocities, if lvs \\ \hline\hline \end{tabular*}\end{center}\end{table}



Table 34.10: Free energy file format.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...rgy at current $\lambda$\ \\ \hline\hline \end{tabular*}\end{center}\end{table}



Table 34.11: Root mean square deviation file format.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...ion after superimposition \\ \hline\hline \end{tabular*}\end{center}\end{table}



Table 34.12: Property file format.
\begin{table}\begin{center} \begin{tabular*}{150mm}{p{15mm}p{12mm}l} \hline\hlin... ...12.5) & value of property \\ \hline\hline \end{tabular*}\end{center}\end{table}


next up previous contents
Next: 35. Pseudopotential plane-wave density Up: user Previous: 33. Combined quantum and   Contents
2003-10-08