From ca575e395e875d59300e11520cc8e634cf1d1283 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 19 Mar 2025 20:39:06 -0400 Subject: [PATCH] fix spelling and duplicate references issues --- doc/src/Howto_moltemplate.rst | 30 ++++++++++----------- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 16 insertions(+), 15 deletions(-) diff --git a/doc/src/Howto_moltemplate.rst b/doc/src/Howto_moltemplate.rst index b8c021ceef..470f76ded0 100644 --- a/doc/src/Howto_moltemplate.rst +++ b/doc/src/Howto_moltemplate.rst @@ -1,16 +1,16 @@ Moltemplate Tutorial ==================== -In this tutorial, we are going to use the tool :ref:`Moltemplate` -to set up a classical molecular dynamic simulation using -the :ref:`OPLS-AA force field `. 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 +` from https://moltemplate.org/ to set up a classical +molecular dynamic simulation using the :ref:`OPLS-AA force field +`. 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) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 084f7c0ec1..baf20a8ebf 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1336,6 +1336,7 @@ Gflop gfortran ghostneigh ghostwhite +Ghahremanpour Giacomo GiB gif