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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.

Openmm.org

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OpenMM - CC Doc

Introduction. OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that makes it unique among MD simulation packages.

Docs.computecanada.ca

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OpenMM - CC Doc

OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that makes it unique among MD simulation packages. Running …

Docs.computecanada.ca

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openmm — openff-interchange documentation

Get_openmm_energies. Given an OpenFF Interchange object, return single-point energies as computed by OpenMM.

Docs.openforcefield.org

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OpenMM interface — Ash 0.1 documentation

Docs » OpenMM interface; Edit on GitHub ; OpenMM interface¶ OpenMM is an open-source molecular mechanics library written in C++. ASH features a flexible interface to the Python API of the OpenMM library. OpenMM has been designed to run on both CPU and GPU codes with the GPU code being particulary fast. The OpenMMTheory class¶ OpenMM can run either on the …

Ash.readthedocs.io

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Contents — UFED for OpenMM documentation

Read the Docs v: latest . Versions latest Downloads pdf html epub On Read the Docs Project Home Builds

Ufedmm.readthedocs.io

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OpenMM - Research Computing Documentation

Description. From the OpenMM web site: OpenMM is an extensible library that enables accelerated calculations for molecular dynamics on high-performance computer architectures, currently for high-end NVIDIA and ATI GPU cards.OpenMM provides tools for modern molecular modeling simulation. As a library it can be hooked into any code, allowing that code to do …

Wiki.rc.usf.edu

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GitHub - openmm/openmm: OpenMM is a toolkit for molecular …

OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.

Github.com

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OpenMM — Bede Documentation

OpenMM# OpenMM is a high-performance toolkit for molecular simulation. It can be used as an application, a library, or a flexible programming environment and includes extensive language bindings for Python, C, C++, and even Fortran. On Bede, OpenMM is made available through the HECBioSim Project. # Load the hecbiosim project module load hecbiosim # Load the desired …

Bede-documentation.readthedocs.io

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OpenMMTools — openmmtools documentation - Read the Docs

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine. openmmtools is a Python library layer that sits on top of OpenMM to provide access to a variety of useful tools for building full-featured molecular simulation packages. high-quality Langevin integrators, including g-BAOAB, VVVR, and other splittings.

Openmmtools.readthedocs.io

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Creating a cgmodel — cg_openmm documentation

Creating a cgmodel. The CGModel object contains the topology, force field definitions, and initial particle positions of a coarse-grained model. The following example creates a homo-oligomer model with 1 backbone bead and 1 sidechain bead per residue. Particle positions are generated using the random builder included in cg_openmm.

Cg-openmm.readthedocs.io

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Index — cg_openmm documentation

Bin_samples() (in module cg_openmm.parameters.reweight) bootstrap_free_energy_folding() (in module cg_openmm.parameters.free_energy) bootstrap_heat_capacity() (in ...

Cg-openmm.readthedocs.io

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OpenMM — CSD3 1.0 documentation

OpenMM is 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.

Docs.hpc.cam.ac.uk

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cg_openmm.parameters.reweight — cg_openmm documentation

Cg_openmm.parameters.reweight Source code for cg_openmm.parameters.reweight import numpy as np from math import exp , log # OpenMM utilities import mdtraj as md import simtk.unit as unit import pymbar from pymbar import timeseries from scipy import interpolate from scipy.optimize import minimize , minimize_scalar , Bounds , LinearConstraint from matplotlib …

Cg-openmm.readthedocs.io

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OpenMM Reporters — MDTraj 1.9.4 documentation

Docs » OpenMM Reporters; View page source; OpenMM Reporters¶ MDTraj provides a few flexible reporters for use with the OpenMM python app. OpenMM is a toolkit for molecular simulation using high performance GPU code. OpenMM itself ships with a DCD reporter, but it lacks the ability to, for instance, report on only a subset of the atoms, which might be desired …

Mdtraj.org

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Python tutorials for OpenMM - GitHub

Python tutorials for OpenMM. This guide is a set of Jupyter notebooks intended to help researchers already familiar with molecular dynamics simulation learn how to use OpenMM in their research and software projects.. Getting started. We recommend you use miniconda and the conda package manager. If you don't already have miniconda installed, you can easily install it …

Github.com

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Integrators — openmmtools documentation - Read the Docs

Warning. OpenMM’s CompoundIntegrator caches OpenMM Integrator objects, but can only return the SWIG-wrapped base integrator object if you call CompoundIntegrator.getIntegrator() or CompoundIntegrator.getCurrentIntegrator().If you want to hold onto one of the Python subclasses we make available in openmmtools.integrators, you will need to cache the original Python …

Openmmtools.readthedocs.io

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OMMProtocol 0.1.13+5.g3105cd3.dirty documentation - Read the …

A command line application to launch molecular dynamics simulations with OpenMM. No coding required - just a YAML input file! Smart support for different input file formats: Topology: PDB/PDBx, Mol2, Amber’s PRMTOP, Charmm’s PSF, Gromacs’ TOP, Desmond’s DMS; Positions: PDB, COOR, INPCRD, CRD, GRO, DCD; Velocities: PDB, VEL

Ommprotocol.readthedocs.io

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Openmm :: Anaconda.org

Anaconda.org

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Docker Hub

Docker Pull Command. Source Repository. Github. matsunagalab/docker-openmm. Why Docker. Overview What is a Container. Products. Product Overview. Product Offerings

Hub.docker.com

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