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fix spelling and duplicate references issues

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Axel Kohlmeyer
2025-03-19 20:39:06 -04:00
parent 37248a011e
commit ca575e395e
2 changed files with 16 additions and 15 deletions
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doc/src/Howto_moltemplate.rst
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@ -1,16 +1,16 @@
Moltemplate Tutorial
====================
In this tutorial, we are going to use the tool :ref:`Moltemplate<moltemplate>`
to set up a classical molecular dynamic simulation using
the :ref:`OPLS-AA force field <oplsaa2024>`. The first
task is to describe an organic compound and create a complete input deck
for LAMMPS. The second task is to use moltemplate to build a polymer.
The third task is to map the OPLS-AA force field to a
molecular sample created with an external tool, e.g. PACKMOL, and
exported as a PDB file. The files used in this tutorial can be found
in the ``tools/moltemplate/tutorial-files`` folder of the LAMMPS
source code distribution.
In this tutorial, we are going to use the tool :ref:`Moltemplate
<Moltemplate1>` from https://moltemplate.org/ to set up a classical
molecular dynamic simulation using the :ref:`OPLS-AA force field
<oplsaa2024>`. The first task is to describe an organic compound and
create a complete input deck for LAMMPS. The second task is to use
moltemplate to build a polymer. The third task is to map the OPLS-AA
force field to a molecular sample created with an external tool,
e.g. PACKMOL, and exported as a PDB file. The files used in this
tutorial can be found in the ``tools/moltemplate/tutorial-files`` folder
of the LAMMPS source code distribution.
Many more examples can be found here: https://moltemplate.org/examples.html
@ -179,7 +179,7 @@ Compile the master file with:
moltemplate.sh solv_01.lt
cleanup_moltemplate.sh # <-- optional: see below
(Note: The optioinal "cleanup_moltemplate.sh" command deletes
(Note: The optional "cleanup_moltemplate.sh" command deletes
unused atom types, which sometimes makes LAMMPS run faster.
But it does not work with many-body pair styles or dreiding-style h-bonds.
Fortunately most force fields, including OPLSAA, don't use those features.)
@ -201,7 +201,7 @@ Then execute the simulation with the following:
Building a simple polymer
"""""""""""""""""""""""""
Moltemplate is particularly useful for building polymers (and other molecules
with subunits). As an simple example, consider butane:
with sub-units). As an simple example, consider butane:
.. figure:: JPG/butane.jpg
@ -224,7 +224,7 @@ The ``butane.lt`` file below defines Butane as a polymer containing
# (Using "$mol:..." indicates this object ("CH3") is part of a larger
# molecule. Moltemplate will share the molecule-ID with that molecule.)
# A list of the bonds within the "CH3" molecular subunit:
# A list of the bonds within the "CH3" molecular sub-unit:
# BondID AtomID1 AtomID2
write('Data Bond List') {
$bond:ch1 $atom:c $atom:h1
@ -242,7 +242,7 @@ The ``butane.lt`` file below defines Butane as a polymer containing
$atom:h2 $mol:... @atom:60 0.0 0.000000 1.0741603 -0.892431
}
# A list of the bonds within the "CH2" molecular subunit:
# A list of the bonds within the "CH2" molecular sub-unit:
# BondID AtomID1 AtomID2
write('Data Bond List') {
$bond:ch1 $atom:c $atom:h1
@ -489,6 +489,6 @@ And execute the simulation with the following:
**(OPLS-AA)** Jorgensen, W.L., Ghahremanpour, M.M., Saar, A., Tirado-Rives, J., J. Phys. Chem. B, 128(1), 250-262 (2024).
.. _Moltemplate:
.. _Moltemplate1:
**(Moltemplate)** Jewett et al., J. Mol. Biol., 433(11), 166841 (2021)

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doc/utils/sphinx-config/false_positives.txt
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@ -1336,6 +1336,7 @@ Gflop
gfortran
ghostneigh
ghostwhite
Ghahremanpour
Giacomo
GiB
gif