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Commit e9021971 authored by Lee-Ping's avatar Lee-Ping
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Merge branch 'amoeba' of github.com:peastman/openmm

parents 25ea315c 075e56ba
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docs/usersguide/application.rst
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...@@ -654,13 +654,15 @@ For the main force field, OpenMM provides the following options: ...@@ -654,13 +654,15 @@ For the main force field, OpenMM provides the following options:
================= ================================================================================ ================= ================================================================================
File Force Field File Force Field
================= ================================================================================ ================= ================================================================================
amber96.xml AMBER96\ :cite:`Kollman1997` amber96.xml AMBER96\ :cite:`Kollman1997`
amber99sb.xml AMBER99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006` amber99sb.xml AMBER99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006`
amber99sbildn.xml AMBER99SB plus improved side chain torsions\ :cite:`Lindorff-Larsen2010` amber99sbildn.xml AMBER99SB plus improved side chain torsions\ :cite:`Lindorff-Larsen2010`
amber99sbnmr.xml AMBER99SB with modifications to fit NMR data\ :cite:`Li2010` amber99sbnmr.xml AMBER99SB with modifications to fit NMR data\ :cite:`Li2010`
amber03.xml AMBER03\ :cite:`Duan2003` amber03.xml AMBER03\ :cite:`Duan2003`
amber10.xml AMBER10 amber10.xml AMBER10
amoeba2009.xml AMOEBA\ :cite:`Ren2002` amoeba2009.xml AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is
recommended to use AMOEBA 2013 instead.
amoeba2013.xml AMOEBA 2013\ :cite:`Shi2013`
================= ================================================================================ ================= ================================================================================
...@@ -692,15 +694,16 @@ the following files: ...@@ -692,15 +694,16 @@ the following files:
.. tabularcolumns:: |l|L| .. tabularcolumns:: |l|L|
================= ============================================================================================== ================= =================================================================================================
File Implicit Solvation Model File Implicit Solvation Model
================= ============================================================================================== ================= =================================================================================================
amber96_obc.xml GBSA-OBC solvation model\ :cite:`Onufriev2004` for use with AMBER96 force field amber96_obc.xml GBSA-OBC solvation model\ :cite:`Onufriev2004` for use with AMBER96 force field
amber99_obc.xml GBSA-OBC solvation model for use with AMBER99 force fields amber99_obc.xml GBSA-OBC solvation model for use with AMBER99 force fields
amber03_obc.xml GBSA-OBC solvation model for use with AMBER03 force field amber03_obc.xml GBSA-OBC solvation model for use with AMBER03 force field
amber10_obc.xml GBSA-OBC solvation model for use with AMBER10 force field amber10_obc.xml GBSA-OBC solvation model for use with AMBER10 force field
amoeba2009_gk.xml Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA force field amoeba2009_gk.xml Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA 2009 force field
================= ============================================================================================== amoeba2013_gk.xml Generalized Kirkwood solvation model for use with AMOEBA 2013 force field
================= =================================================================================================
For example, to use the GBSA-OBC solvation model with the Amber99SB force field, For example, to use the GBSA-OBC solvation model with the Amber99SB force field,
......
docs/usersguide/references.bib
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...@@ -336,10 +336,20 @@ ...@@ -336,10 +336,20 @@
type = {Journal Article} type = {Journal Article}
} }
@article{Shi2013
author = {Shi, Yue and Xia, Zhen and Zhang, Jiajing and Best, Robert and Wu, Chuanjie and Ponder, Jay W. and Ren, Pengyu},
title = {Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {9},
pages = {4046-4063},
year = {2013},
type = {Journal Article}
}
@article{Shirts2007 @article{Shirts2007
author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.}, author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations},
Simulations},
journal = {Journal of Physical Chemistry B}, journal = {Journal of Physical Chemistry B},
volume = {111}, volume = {111},
pages = {13052-13063}, pages = {13052-13063},
......
wrappers/python/simtk/openmm/app/data/amoeba2013.xml 0 → 100644
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wrappers/python/simtk/openmm/app/data/amoeba2013_gk.xml 0 → 100644
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