2016
DOI: 10.1101/091801
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OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics

Abstract: OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itsel… Show more

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Cited by 318 publications
(421 citation statements)
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“…Simulations for parameterization. All the MD simulations for the ion model parameterization were performed with OpenMM (version 7.0.1) 44 , as the package is highly flexible and can be easily customized with a Python interface, and the CHARMM force field 45 (version C36_Aug15) was utilized in this work.…”
Section: Methodsmentioning
confidence: 99%
“…Simulations for parameterization. All the MD simulations for the ion model parameterization were performed with OpenMM (version 7.0.1) 44 , as the package is highly flexible and can be easily customized with a Python interface, and the CHARMM force field 45 (version C36_Aug15) was utilized in this work.…”
Section: Methodsmentioning
confidence: 99%
“…Equilibration and production MD simulation details. The MD simulations were performed using OpenMM 7.1.1 35 . We used a Langevin integrator with 2 fs time step and a friction coefficient of 1 ps −1 .…”
Section: Methodsmentioning
confidence: 99%
“…The system was parameterized using tleap in AmberTools18 63 by ff14SB 64 and LIPID17 force elds, and along with TIP3P water model 65 . All the simulations were performed using OpenMM7 66 . We rst applied positional constraints (k=10 kcal/mol/Å 2 ) on protein heavy atoms for a 5000-step minimization, then released constraints of side-chains when heating up the system to 310 K with 2 fs stepsize (H-bonds constraints), 1 ps-1 friction coe cient for Langevin dynamics, Particle Mesh Ewald (PME) method 67 , and 12 Å non-bonded cutoff.…”
Section: Molecular Dynamics Simulationmentioning
confidence: 99%