Subprograms used:Cat IdTitleReferenceAEEE_v2_0PLUMEDCPC 185 (2014) 604Nature of problem: Compute and visualize values of collective variables on molecular dynamics trajectories from within VMD, and interactively develop biasing scripts for the estimation of free-energy surfaces in PLUMED. Solution ...
IMD (Interactive Molecular Dynamics) is supported natively in GROMACS and VMD. MDDriver is no longer needed for this kind of simulation.MDDriver is compatible with this IMD protocol used by VMD and GROMACS. These 3 components (UnityMol, MDDriver and Biospring) have been used together recently...
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective variables (CVs) and VMD's chemically-aware atom selection language...
3D/VR Interactive EnvironmentMolecular Dynamics (MD) SimulationsNanoscale Materials VisualizationLAMMPSNVIDIA CUDAAccelerated ComputingMaterials ScienceVirtual RealityNanostructuresSilica Glass NanospringsComputational SystemResearch EnvironmentTeaching Instrument
A carbon nanotube model (length: 7.8704 nm; diameter: 2.711 nm) was built using Visual Molecular Dynamics (VMD) software. Then, the obtained nanotube was placed in a rectangle box with dimensions of 8 × 8 × 7.8704 nm3. The nanotube was placed in the center of the box with it...
A membrane is an assembly of phospholipids. Phospholipids structures are created following the process described in the VMD Membrane Proteins tutorial. The assembly itself is generated by the BioExplorer, for a given shape, and a number of instances of phospholipids....
We present a mathematical and computational formulation for constrained dynamics that makes this possible, allowing encapsulated objects, constraints, and forces to be combined dynamically and simulated efficiently. The formulation handles arbitrary objects, including nonrigid bodies. We describe an ...
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