diff --git a/.nojekyll b/.nojekyll
new file mode 100644
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diff --git a/about.html b/about.html
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----
-layout: page
-title: About OpenMM
----
-
-
-
-
-
-
-
About OpenMM
-
- Backed by researchers and developers from Stanford University, MSKCC, UPF, and others around the world.
-
-
-
-
-
-
-
-
-
-
Custom Forces
-
- Want a custom force between two atoms? No problem. Write your force expressions in string format, and OpenMM will generate blazing fast code to do just that. No more hand-writing GPU kernels.
-
-
-
-
Highly Optimized
-
- OpenMM is optimized for the latest generation of compute hardware, including AMD (via OpenCL) and NVIDIA (via CUDA) GPUs. We also heavily optimize for CPUs using intrinsics.
-
-
-
-
Portable
-
- We strive to make our binaries as portable as possible. We've tested OpenMM on many flavors of Linux, OS X, and even Windows.
-
- Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon, Yutong Zhao, Kyle A. Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande. OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics. PLoS Comput. Biol. 13:e1005659, 2017.
-
-
+
+
+ Simulation speed
+
+
+
+
+
+
+ Dihydrofolate Reductase (DHFR)
+
+ OpenMM was benchmarked on the dihydrofolate reductase (DHFR) models taken from the Joint Amber/Charmm benchmark. This is a 159 residue protein with 2489 atoms. The version used for explicit solvent simulations included 7023 TIP3P water molecules, giving a total of 23,558 atoms. All simulations used the AMBER99SB force field and a Langevin integrator, and were run with OpenMM 7.4.
+
+
+
+ Treatment of Solvent
+
+
+ Three different methods were used to calculate the effect of solvent:
+
+
+ Implicit: Solvent was represented with an OBC-GBSA implicit solvent model. Long range interactions were cut off at 2 nm.
+
+
+ Explicit-RF: Solvent was modeled explicitly. Long range interactions were cut off at 1 nm using the reaction field method.
+
+
+ Explicit-PME: Solvent was modeled explicitly. Long range interactions were calculated using Particle Mesh Ewald. The Ewald error tolerance was set to 0.0005, and the direct space cutoff was chosen to optimize performance (0.9 nm for the GPU simulations, 0.8 nm for the CPU simulations).
+
+
+
+
+
+
+ Time Step
+
+
+ Two step sizes were used for the simulations:
+
+
+ 2 fs: For these simulations, the lengths of bonds involving hydrogen were constrained.
+
+
+ 5 fs: For these simulations, the lengths of all bonds were constrained. In addition, mass repartitioning was used to increase the mass of hydrogen atoms to 4 amu.
+
+
+ Water molecules were fully rigid in all cases, and the constraint error tolerance was set to 0.00001.
+
+
+
+
+ Platforms
+
+
+ Simulations were run using the following platforms and hardware:
+
+
CUDA platform on an NVIDIA Titan X Pascal GPU.
+
CUDA platform on an NVIDIA Titan V GPU.
+
OpenCL platform on NVIDIA Titan X Pascal GPU.
+
OpenCL platform on NVIDIA Titan V GPU.
+
OpenCL platform on an AMD Radeon RX 5700 XT GPU.
+
CPU platform on a 4 core 4.3 GHz Intel Core i7-7740X CPU.
+
+ Water molecules were fully rigid in all cases, and the constraint error tolerance was set to 0.00001.
+
+
+
+
+
+
+
+
+ More benchmarks
+
+
+
+
+
\ No newline at end of file
diff --git a/development.vue b/development.vue
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@@ -0,0 +1,100 @@
+
+
+
+
+ OpenMM Team
+
+ Researchers and developers actively working on OpenMM.
+
+
+
+
+
+ Markland Lab
+
+
+
+
+
+
+
+ Funding Sources
+
+
+
+
+ Chan Zuckerberg Initiative
+
+ OpenMM is currently (May 2020-Apr 2021) funded by the CZI Essential Open Source Software for Science grant.
+
+
+
+
+
+ OpenMM Consortium
+
+ A community of researchers and developers supporting OpenMM.
+
+
+
+
+
+ {{ person }}
+
+
+
+
+
+
\ No newline at end of file
diff --git a/documentation.html b/documentation.html
deleted file mode 100644
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----
-layout: page
-title: OpenMM Documentation
----
-
-
-
-
-
-
Documentation
-
Resources for finding your way around OpenMM.
-
-
-
-
-
-
-
-
-
-
Getting Started
-
The easiest way to get started is to familiarize yourself with the User Guide, which contains basics about installing OpenMM, making sure that it runs smoothly, and running a couple of example simulations.
- The C++ API provides information about OpenMM's C++ interface.
-
-
-
-
-
Workshop Videos
-
Every year, we hold several OpenMM workshops at Stanford University. After you have successfully installed OpenMM, here are some introductory videos from previous workshops.
- The C++ API provides information about OpenMM's C++ interface.
-
-
-
-
-
-
-
-
diff --git a/documentation.vue b/documentation.vue
new file mode 100644
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--- /dev/null
+++ b/documentation.vue
@@ -0,0 +1,176 @@
+
+
+
+
+ Getting Started
+
+ The easiest way to get started is to familiarize yourself with the User Guide, which contains basics about installing OpenMM, making sure that it runs smoothly, and running a couple of example simulations.
+
+
+
+
+
+ User Guide
+
+ Start here if it's your first time using OpenMM. These documents will get you up and running simulations in short order.
+
+
+
+ Developer Guide
+
+ This section provides in-depth information on the code-base and how to contribute to the development of OpenMM itself.
+
+
+
+ Python API
+
+ The Python API provides information about the classes and methods available to Python developers.
+
+
+
+ C++ API
+
+ The C++ API provides information about OpenMM's C++ interface.
+
+
+
+
+
+ Workshop Videos
+
+ Every year, we hold several OpenMM workshops at Stanford University. After you have successfully installed OpenMM, here are some introductory videos from previous workshops.
+
+
+
+
+
+ OpenMM Workshop 2012
+
+
+
+
+
+
+
+ OpenMM Workshop 2013
+
+
+
+
+
+
+
+ OpenMM Workshop 2014
+
+
+
+
+
+
+
+
+
+ Support
+
+ For bug reports, feature requests, specific questions, etc.
+
+
+
+
+
+ FAQ
+
+ Frequently asked questions about OpenMM.
+
+
+
+ Issue Tracker
+
+ Report bugs and request features. Please describe clearly what you want to achieve.
+
+
+
+ Forum (old)
+
+ General discussion how to use OpenMM.
+
+
+
+ Hardware (old)
+
+ Hardware requiment and recommendations for OpenMM.
+
+
+
+
+
+ Publications
+
+ If you use OpenMM for scientific research, please cite it.
+
+
+
+
+
+
+ Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon, Yutong Zhao, Kyle A. Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande. OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics. PLoS Comput. Biol. 13:e1005659, 2017. DOI: 10.1371/journal.pcbi.1005659
+
+
+
+
+ More publications
+
+
+
+ Bleeding Edge
+
+ Visit the OpenMM repository at GitHub to stay up to date with the latest development.
+
+
+
+
+
+ User Guide (dev)
+
+ Start here if it's your first time using OpenMM. These documents will get you up and running simulations in short order.
+
+
+
+ Developer Guide (dev)
+
+ This section provides in-depth information on the code-base and how to contribute to the development of OpenMM itself.
+
+
+
+ Python API (dev)
+
+ The Python API provides information about the classes and methods available to Python developers.
+
+
+
+ C++ API (dev)
+
+ The C++ API provides information about OpenMM's C++ interface.
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/ecosystem.vue b/ecosystem.vue
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@@ -0,0 +1,153 @@
+
+
+
+
+ Built with OpenMM
+
+ Trusted and used by scientists around the world.
+
+
+
+
+
+ ACEMD
+
+ The next generation molecular dynamic simulation engine designed to accelerate drug discovery process by providing all necessary capabilities.
+
+
+
+ CHARMM
+
+ A molecular simulation program with many energy functions, enhanced
+ sampling methods, implicit solvent models, and support for multi-scale
+ modeling.
+
+
+
+ Folding@home
+
+ A distributed computing project for simulating protein dynamics, including the process of protein folding and the movements of proteins implicated in a variety of diseases.
+
+
+
+ ForceBalance
+
+ A powerful and highly versatile software package for force field optimization.
+
+
+
+ GPUGRID.net
+
+ A distributed computing infrastructure devoted to biomedical research to understand the function of biomolecules for health and disease.
+
+
+
+ GROMACS
+
+ a molecular dynamics package mainly designed for simulations of
+ proteins, lipids, and nucleic acids.
+
+
+
+ PDBFixer
+
+ A powerful, flexible tool for preparing PDB files for molecular simulation or modeling, capable of running in interactive, Python-scriptable, or fully automated modes.
+
+
+
+ SireMol
+
+ An advanced, multiscale, molecular simulation framework. It allows
+ to quickly prototype and develop new algorithms.
+
+
+
+ TINKER
+
+ A high-performance molecular modeling and simulation platform.
+
+
+
+ YANK
+
+ A GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations.
+
+
+
+
+
+ OpenMM Plugins
+
+ Expand OpenMM capabilities by interfacing with other software. The plugins are developed
+ and released independetly from OpenMM.
+
+
+
+
+
+ OpenMM-PLUMED
+
+ Provides a connection between OpenMM and PLUMED. It allows you to bias or analyze an OpenMM simulation based on collective variables.
+
+
+
+ OpenMM-TensorFlow
+
+ This is a plugin for OpenMM that allows neural networks to be used for defining forces. It is implemented with TensorFlow.
+
+
+
+ OpenMM-TensorRT
+
+ This is a plugin for OpenMM that allows neural networks to be used for defining forces. It is implemented with TensorRT.
+
+
+
+ OpenMM-Torch
+
+ A plugin for OpenMM that allows PyTorch static computation graphs to be used for defining an OpenMM force object.
+
+
+
+
+
+ OpenMM Tools
+
+ Resources that make it easier to use OpenMM.
+
+
+
+
+
+ OpenMMTools
+
+ Integrators, enhanced sampling methods, test systems, and alchemical factories for OpenMM.
+
+
+
+ OpenMM Setup
+
+ A graphical application to set up and run simulations with OpenMM. Includes pull-down menus, pop-up tips, error checking, and live script building
+
+
+
+ OpenMM-MD
+
+ A general purpose script (with lots of comments) that uses the OpenMM Python module to drive MD simulations. Simulation options are handled via an input file.
+
+
+
+ PME Optimizer
+
+ A script to optimize the performance of PME. It runs a series of simulations and selects the parameters that give best performance for simulating a particular system on particular hardware.
+
+
+
+ Omnia
+
+ An open source ecosystem built around OpenMM.
+
+
+
+
+
\ No newline at end of file
diff --git a/example.py b/example.py
new file mode 100644
index 0000000..e8d265d
--- /dev/null
+++ b/example.py
@@ -0,0 +1,15 @@
+from simtk.openmm.app import *
+from simtk.openmm import *
+from simtk.unit import *
+from sys import stdout
+
+pdb = PDBFile('input.pdb')
+forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
+system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
+integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
+simulation = Simulation(pdb.topology, system, integrator)
+simulation.context.setPositions(pdb.positions)
+simulation.minimizeEnergy()
+simulation.reporters.append(PDBReporter('output.pdb', 1000))
+simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True))
+simulation.step(10000)
\ No newline at end of file
diff --git a/home.vue b/home.vue
new file mode 100644
index 0000000..effd105
--- /dev/null
+++ b/home.vue
@@ -0,0 +1,61 @@
+
+
+
+
+
+
+ Want a custom force between two atoms? No problem. Write your force expressions in string format, and OpenMM will generate blazing fast code to do just that. No more hand-writing GPU kernels.
+
+
+ OpenMM is optimized for the latest generation of compute hardware, including AMD (via OpenCL) and NVIDIA (via CUDA) GPUs. We also heavily optimize for CPUs using intrinsics.
+
+
+ We strive to make our binaries as portable as possible. We've tested OpenMM on many flavors of Linux, OS X, and even Windows.
+
+
+ Install OpenMM and all its dependencies with Conda package manager. No manual compilation
+ from source required.
+
+
+
+
+ mdi-play-circle-outline
+ Run in Colab
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/index.html b/index.html
index c27eaca..b076e5c 100644
--- a/index.html
+++ b/index.html
@@ -1,80 +1,108 @@
----
-layout: page
-title: OpenMM
----
-
-
-
-
-
-
-
-
-
-
OpenMM
-
- A high performance toolkit for molecular simulation. Use it as a library, or as an application. We include extensive language bindings for Python, C, C++, and even Fortran. The code is open source and actively maintained on Github, licensed under MIT and LGPL. Part of the Omnia suite of tools for predictive biomolecular simulation.
-
- Extreme flexibility through custom forces and integrators. Extreme performance through GPU Acceleration, with optimizations for AMD, NVIDIA, and Intel Integrated GPUs. It's fast on CPUs too. See the benchmarks.
-
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/news.vue b/news.vue
new file mode 100644
index 0000000..3bd97d9
--- /dev/null
+++ b/news.vue
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+ Read Tweets
+
+
+
+
+
\ No newline at end of file
diff --git a/resources.html b/resources.html
deleted file mode 100644
index 4ecd87a..0000000
--- a/resources.html
+++ /dev/null
@@ -1,33 +0,0 @@
----
-layout: page
-title: Resources
----
-
-
-
-
-
-
-
Resources
-
Resources that make it easier to use OpenMM.
-
-
-
-
-
-
-
-
-
-
The OpenMM team has reviewed the links on this page, but we encourage the community to add their own.
-
Tools
-
Omnia An open source ecosystem built around OpenMM.
-
OpenMMTools Integrators, enhanced sampling methods, test systems, and alchemical factories for OpenMM.
-
OpenMM Setup A graphical application to set up and run simulations with OpenMM. Includes pull-down menus, pop-up tips, error checking, and live script building capabilities.
-
PME Optimizer A script to optimize the performance of PME. It runs a series of simulations and selects the parameters that give best performance for simulating a particular system on particular hardware.
-
OpenMM-MD A general purpose script (with lots of comments) that uses the OpenMM Python module to drive MD simulations. Simulation options are handled via an input file. To facilitate use of the script, the available options are always printed out for you to see, along with documentation.
-
-
-
-
diff --git a/slide.vue b/slide.vue
new file mode 100644
index 0000000..cb7de68
--- /dev/null
+++ b/slide.vue
@@ -0,0 +1,14 @@
+
+
+
+ {{ title }}
+
+
+
+
+
+
\ No newline at end of file
diff --git a/support.html b/support.html
deleted file mode 100644
index 0f9492b..0000000
--- a/support.html
+++ /dev/null
@@ -1,29 +0,0 @@
----
-layout: page
-title: OpenMM Support
----
-
-
-
-
-
-
Support
-
For help on submitting bug reports, requesting features, etc.
-
-
-
-
-
-
-
-
-
Users
-
Use the Issue Tracker to file bug reports. Please include as much information about your hardware, simulation parameters, and system as possible. It is highly recommended to included serialized XML files of your System, Integrator, and State objects.
-
For general help on how to use OpenMM, check out our forum or refer to our FAQ for common errors.
-
If you'd like to request a new feature to be included into the next version of OpenMM, please use the Issue Tracker. Note that we have a review process, and while we will consider all requests, we cannot guarantee that they will be implemented.
We encourage developers to use our Github Repository's Issue Tracker. Note that the discussion is highly technical and is not suitable for most users.
-
-
-
diff --git a/top.vue b/top.vue
new file mode 100644
index 0000000..3a0acdf
--- /dev/null
+++ b/top.vue
@@ -0,0 +1,15 @@
+
+
+
+
+
+
+ OpenMM
+
+ A high-performance toolkit for molecular simulation.
+ Use it as a library, or as an application. We include extensive language bindings for Python, C, C++, and even Fortran.
+ The code is open source and developed on GitHub, licensed under MIT and LGPL.
+
+
+
+
\ No newline at end of file
diff --git a/tutorial.vue b/tutorial.vue
new file mode 100644
index 0000000..d909b08
--- /dev/null
+++ b/tutorial.vue
@@ -0,0 +1,17 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/tutorials.vue b/tutorials.vue
new file mode 100644
index 0000000..f64ad0c
--- /dev/null
+++ b/tutorials.vue
@@ -0,0 +1,56 @@
+
+
+
+
+ OpenMM Cookbook and Tutorials
+
+ Tutorials and examples for quickly getting started with OpenMM
+
+
+
+
+
+
+ {{ tutorial.title }}
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/tutorials/alchemical-free-energy/index.md b/tutorials/alchemical-free-energy/index.md
index ce3959b..275f154 100644
--- a/tutorials/alchemical-free-energy/index.md
+++ b/tutorials/alchemical-free-energy/index.md
@@ -1,9 +1,8 @@
----
-layout: nicepage
-title: Alchemical free energy calculations
-lead: Computing the free energy of inserting a Lennard-Jones particle in a Lennard-Jones fluid
----
+# Alchemical free energy calculations
+*Computing the free energy of inserting a Lennard-Jones particle in a Lennard-Jones fluid.*
+
+This tutorial is described in [OpenMM 7](http://dx.doi.org/10.1371/journal.pcbi.1005659) publication.
## Files
The code for this example can be downloaded here:
diff --git a/tutorials/b2ar_membrane/charmm_example.md b/tutorials/b2ar_membrane/charmm_example.md
index 261996b..b9dafdf 100644
--- a/tutorials/b2ar_membrane/charmm_example.md
+++ b/tutorials/b2ar_membrane/charmm_example.md
@@ -1,7 +1,4 @@
----
-layout: nicepage
-title: Using CHARMM input files in OpenMM and a CHARMM-GUI example
----
+# Using CHARMM input files in OpenMM and a CHARMM-GUI example
OpenMM can directly read CHARMM input files through the use of the `simtk.openmm.app` layer. This enables the use of all
the powerful setup tools in the CHARMM ecosystem that a user might be familiar with such as the [CHARMM-GUI](http://onlinelibrary.wiley.com/doi/10.1002/jcc.20945/abstract), [VMD](http://www.sciencedirect.com/science/article/pii/0263785596000185?via%3Dihub), [CGenFF program](https://cgenff.paramchem.org/)
diff --git a/tutorials/b2ar_membrane/index.md b/tutorials/b2ar_membrane/index.md
index f971f8d..6697a52 100644
--- a/tutorials/b2ar_membrane/index.md
+++ b/tutorials/b2ar_membrane/index.md
@@ -1,9 +1,8 @@
----
-layout: nicepage
-title: Using OpenMM 7 to simulate the beta-2-adrenergic receptor
-lead: Use CHARMM-GUI to set up a membrane protein simulation for OpenMM
+# Beta-2-adrenergic receptor (B2AR) membrane protein simulation with CHARMM
----
+*Use CHARMM-GUI to set up a membrane protein simulation for OpenMM.*
+
+This tutorial is described in [OpenMM 7](http://dx.doi.org/10.1371/journal.pcbi.1005659) publication.
## Files
diff --git a/tutorials/hkmt_tip4pew/index.md b/tutorials/hkmt_tip4pew/index.md
index 7fd7a00..d81b932 100644
--- a/tutorials/hkmt_tip4pew/index.md
+++ b/tutorials/hkmt_tip4pew/index.md
@@ -1,8 +1,8 @@
----
-layout: nicepage
-title: Simulating a histone methyltransferase with TIP4P-Ew
-lead: Simulating a protein with a multisite water model
----
+# Histone methyltransferase simulation with a multisite water model (TIP4P-Ew)
+
+*Simulating a protein with a multisite water model.*
+
+This tutorial is described in [OpenMM 7](http://dx.doi.org/10.1371/journal.pcbi.1005659) publication.
## Files
diff --git a/tutorials/hkmt_zinc/index.md b/tutorials/hkmt_zinc/index.md
index 594011d..2a3720e 100644
--- a/tutorials/hkmt_zinc/index.md
+++ b/tutorials/hkmt_zinc/index.md
@@ -1,8 +1,8 @@
----
-layout: nicepage
-title: Simulating a histone methyltransferase with structural Zn2+ ions
-lead: Simulating a protein with structural zinc ions using multisite ions
----
+# Histone methyltransferase simulation with multisite Zn2+ structural ions
+
+*Simulating a protein with structural zinc ions using multisite ions.*
+
+This tutorial is described in [OpenMM 7](http://dx.doi.org/10.1371/journal.pcbi.1005659) publication.
## Files
diff --git a/tutorials/hsp90_adp_mg/index.md b/tutorials/hsp90_adp_mg/index.md
index fe2ca8a..e68a5fd 100644
--- a/tutorials/hsp90_adp_mg/index.md
+++ b/tutorials/hsp90_adp_mg/index.md
@@ -1,8 +1,6 @@
----
-layout: nicepage
-title: Simulating HSP90 with ADP:Mg2+
-lead: Simulating a protein:ligand complex with multisite solvated ions
----
+# HSP90 with ADP:Mg2+ simulation
+
+*Simulating a protein:ligand complex with multisite solvated ions.*
## Files
@@ -110,7 +108,7 @@ quit
os.system('tleap -f leaprc.hsp90')
```
-```
+```plaintext
> python zeroBvalues.py
This is a simple script designed to zero out the Lennard-Jones
-