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Merge pull request #4201 from lammps/amoeba-doc-page

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Fix errors in fix amoeba/pitorsion doc page
This commit is contained in:
Axel Kohlmeyer
2024-06-21 12:17:26 -04:00
committed by GitHub
parent 241a8dda63 d0da16070b
commit 13f0e37a57
3 changed files with 27 additions and 23 deletions
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23
doc/src/fix_amoeba_bitorsion.rst
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@ -35,7 +35,11 @@ the implementation of AMOEBA and HIPPO in LAMMPS.
Bitorsion interactions add additional potential energy contributions
to pairs of overlapping phi-psi dihedrals of amino-acids, which are
important to properly represent their conformational behavior.
important to properly represent their conformational behavior. Each
bitorsion interaction is thus defined for a 5-tuple of atoms
:math:`IJKLM` with bonds between successive atoms in the list,
i.e. two overlapping dihedral interactions for atoms :math:`IJKL` and
:math:`JKLM`.
The examples/amoeba directory has a sample input script and data file
for ubiquitin, which illustrates use of the fix amoeba/bitorsion
@ -68,14 +72,15 @@ lines:
[...]
N 3 314 315 317 318 330
The first column is an index from 1 to :math:`N` to enumerate the bitorsion
5-atom tuples; it is ignored by LAMMPS. The second column is the
*type* of the interaction; it is an index into the bitorsion force
field file. The remaining 5 columns are the atom IDs of the atoms in
the two 4-atom dihedrals that overlap to create the bitorsion 5-body
interaction. Note that the *bitorsions* and *BiTorsions* keywords for
the header and body sections match those specified in the
:doc:`read_data <read_data>` command following the data file name.
The first column is an index from 1 to :math:`N` to enumerate the
bitorsion 5-atom tuples; it is ignored by LAMMPS. The second column
is the *type* of the interaction; it is an index into the bitorsion
force field file. The remaining 5 columns are the atom IDs of the
atoms (in order) for the 5-tuple :math:`IJKLM`, as described above.
Note that the *bitorsions* and *BiTorsions* keywords for the header
and body sections match those specified in the :doc:`read_data
<read_data>` command following the data file name.
The data file should be generated by using the
tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS

23
doc/src/fix_amoeba_pitorsion.rst
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@ -57,7 +57,7 @@ should have two lines like these in its header section:
M pitorsion types
N pitorsions
where :math:`N` is the number of pitorsion 5-body interactions and :math:`M` is
where :math:`N` is the number of pitorsion 6-body interactions and :math:`M` is
the number of pitorsion types. It should also have two sections in the body
of the data file like these with :math:`M` and :math:`N` lines each:
@ -74,21 +74,20 @@ of the data file like these with :math:`M` and :math:`N` lines each:
PiTorsions
1 1 8 10 12 18 20
2 5 18 20 22 25 27
1 1 2 4 3 20 21 24
2 5 21 23 22 37 38 41
[...]
N 3 314 315 317 318 330
N 7 27 29 28 30 35 36
For PiTorsion Coeffs, the first column is an index from 1 to :math:`M` to
enumerate the pitorsion types. The second column is the single
For PiTorsion Coeffs, the first column is an index from 1 to :math:`M`
to enumerate the pitorsion types. The second column is the single
prefactor coefficient needed for each type.
For PiTorsions, the first column is an index from 1 to :math:`N` to enumerate
the pitorsion 5-atom tuples; it is ignored by LAMMPS. The second
column is the "type" of the interaction; it is an index into the
PiTorsion Coeffs. The remaining 5 columns are the atom IDs of the
atoms in the two 4-atom dihedrals that overlap to create the pitorsion
5-body interaction.
For PiTorsions, the first column is an index from 1 to :math:`N` to
enumerate the pitorsion 6-atom tuples; it is ignored by LAMMPS. The
second column is the "type" of the interaction; it is an index into
the PiTorsion Coeffs. The remaining 6 columns are the atom IDs of the
atoms (in order) for the 6-tuple :math:`IJKLMN`, as described above.
Note that the *pitorsion types* and *pitorsions* and *PiTorsion
Coeffs* and *PiTorsions* keywords for the header and body sections of