<p>The IDs for the two atoms in each bond should be values
from 1 to Natoms, where Natoms = # of atoms in the molecule.</p>
<hrclass="docutils"/>
<p><em>Angles</em> section:</p>
<ulclass="simple">
<li>one line per angle</li>
<li>line syntax: ID type atom1 atom2 atom3</li>
<li>type = angle type (1-Nangletype)</li>
<li>atom1,atom2,atom3 = IDs of atoms in angle</li>
</ul>
<p>The IDs for the three atoms in each angle should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are
ordered linearly within the angle. Thus the central atom (around
which the angle is computed) is the atom2 in the list.</p>
<hrclass="docutils"/>
<p><em>Dihedrals</em> section:</p>
<ulclass="simple">
<li>one line per dihedral</li>
<li>line syntax: ID type atom1 atom2 atom3 atom4</li>
<li>type = dihedral type (1-Ndihedraltype)</li>
<li>atom1,atom2,atom3,atom4 = IDs of atoms in dihedral</li>
</ul>
<p>The IDs for the four atoms in each dihedral should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are
ordered linearly within the dihedral.</p>
<hrclass="docutils"/>
<p><em>Impropers</em> section:</p>
<ulclass="simple">
<li>one line per improper</li>
<li>line syntax: ID type atom1 atom2 atom3 atom4</li>
<li>type = improper type (1-Nimpropertype)</li>
<li>atom1,atom2,atom3,atom4 = IDs of atoms in improper</li>
</ul>
<p>The IDs for the four atoms in each improper should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The ordering of
the 4 atoms determines the definition of the improper angle used in
the formula for the defined <aclass="reference internal"href="improper_style.html"><spanclass="doc">improper style</span></a>. See
the doc pages for individual styles for details.</p>
<hrclass="docutils"/>
<p><em>Special Bond Counts</em> section:</p>
<ulclass="simple">
<li>one line per atom</li>
<li>line syntax: ID N1 N2 N3</li>
<li>N1 = # of 1-2 bonds</li>
<li>N2 = # of 1-3 bonds</li>
<li>N3 = # of 1-4 bonds</li>
</ul>
<p>N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
this atom within the topology of the molecule. See the
<aclass="reference internal"href="special_bonds.html"><spanclass="doc">special_bonds</span></a> doc page for more discussion of
1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds
section must also appear. If this section is not specied, the
atoms in the molecule will have no special bonds.</p>
<hrclass="docutils"/>
<p><em>Special Bonds</em> section:</p>
<ulclass="simple">
<li>one line per atom</li>
<li>line syntax: ID a b c d ...</li>
<li>a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds</li>
</ul>
<p>A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
1-4 neighbors of this atom. The IDs should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The first N1
values should be the 1-2 neighbors, the next N2 should be the 1-3
neighbors, the last N3 should be the 1-4 neighbors. No atom ID should
appear more than once. See the <aclass="reference internal"href="special_bonds.html"><spanclass="doc">special_bonds</span></a> doc
page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section
appears, the Special Bond Counts section must also appear. If this
section is not specied, the atoms in the molecule will have no special
bonds.</p>
<hrclass="docutils"/>
<p><em>Shake Flags</em> section:</p>
<ulclass="simple">
<li>one line per atom</li>
<li>line syntax: ID flag</li>
<li>flag = 0,1,2,3,4</li>
</ul>
<p>This section is only needed when molecules created using the template
will be constrained by SHAKE via the “fix shake” command. The other
two Shake sections must also appear in the file, following this one.</p>
<p>The meaning of the flag for each atom is as follows. See the <aclass="reference internal"href="fix_shake.html"><spanclass="doc">fix shake</span></a> doc page for a further description of SHAKE
clusters.</p>
<ulclass="simple">
<li>0 = not part of a SHAKE cluster</li>
<li>1 = part of a SHAKE angle cluster (two bonds and the angle they form)</li>
<li>2 = part of a 2-atom SHAKE cluster with a single bond</li>
<li>3 = part of a 3-atom SHAKE cluster with two bonds</li>
<li>4 = part of a 4-atom SHAKE cluster with three bonds</li>
</ul>
<hrclass="docutils"/>
<p><em>Shake Atoms</em> section:</p>
<ulclass="simple">
<li>one line per atom</li>
<li>line syntax: ID a b c d</li>
<li>a,b,c,d = IDs of atoms in cluster</li>
</ul>
<p>This section is only needed when molecules created using the template
will be constrained by SHAKE via the “fix shake” command. The other
two Shake sections must also appear in the file.</p>
<p>The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c,d values identically.</p>
<p>If flag = 0, no a,b,c,d values are listed on the line, just the
(ignored) ID.</p>
<p>If flag = 1, a,b,c are listed, where a = ID of central atom in the
angle, and b,c the other two atoms in the angle.</p>
<p>If flag = 2, a,b are listed, where a = ID of atom in bond with the the
lowest ID, and b = ID of atom in bond with the highest ID.</p>
<p>If flag = 3, a,b,c are listed, where a = ID of central atom,
and b,c = IDs of other two atoms bonded to the central atom.</p>
<p>If flag = 4, a,b,c,d are listed, where a = ID of central atom,
and b,c,d = IDs of other three atoms bonded to the central atom.</p>
<p>See the <aclass="reference internal"href="fix_shake.html"><spanclass="doc">fix shake</span></a> doc page for a further description
of SHAKE clusters.</p>
<hrclass="docutils"/>
<p><em>Shake Bond Types</em> section:</p>
<ulclass="simple">
<li>one line per atom</li>
<li>line syntax: ID a b c</li>
<li>a,b,c = bond types (or angle type) of bonds (or angle) in cluster</li>
</ul>
<p>This section is only needed when molecules created using the template
will be constrained by SHAKE via the “fix shake” command. The other
two Shake sections must also appear in the file.</p>
<p>The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c values identically.</p>
<p>If flag = 0, no a,b,c values are listed on the line, just the
(ignored) ID.</p>
<p>If flag = 1, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the 2nd non-central atom (value c in the Shake Atoms section), and c =
the angle type (1 to Nangletypes) of the angle between the 3 atoms.</p>
<p>If flag = 2, only a is listed, where a = bondtype of the bond between
the 2 atoms in the cluster.</p>
<p>If flag = 3, a,b are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), and b = bondtype of the bond between the central atom
and the 2nd non-central atom (value c in the Shake Atoms section).</p>
<p>If flag = 4, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the 2nd non-central atom (value c in the Shake Atoms section), and c =
bondtype of the bond between the central atom and the 3rd non-central
atom (value d in the Shake Atoms section).</p>
<p>See the <aclass="reference internal"href="fix_shake.html"><spanclass="doc">fix shake</span></a> doc page for a further description
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