• ESPResSo

  • Referenced in 17 articles [sw06335]
  • Dynamics many-particle simulations of ”coarse-grained” bead-spring models as they are used...
  • NFsim

  • Referenced in 11 articles [sw22256]
  • advanced and flexible options for simulating coarse-grained representations of complex nonlinear reaction mechanisms ... found here. NFsim is ideal for modeling polymerization, aggregation, and cooperative reactions that cannot ... simulators. Models are specified in the BioNetGen Langauge, providing a powerful model building environment. Note ... Emonet T. Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nature Methods...
  • MagiC

  • Referenced in 1 article [sw38791]
  • MagiC: Software Package for Multiscale Coarse-Grained Modeling. MagiC is a software package designed ... perform systematic coarse-graining of molecular models for multiscale simulations. MagiC takes input from atomistic ... GROMACS or MDynaMix), creates a coarse-grained trajectory according to a specified mapping scheme, computes ... compute effective potentials for the coarse-grained model. Such potentials can be then further used...
  • VOTCA

  • Referenced in 1 article [sw40481]
  • Coarse-graining Applications (VOTCA) is a Coarse-grained modeling package, which focuses on the analysis ... dynamics data, the development of systematic coarse-graining techniques as well as methods used...
  • RNAexpNumNbors

  • Referenced in 1 article [sw23799]
  • kinetics with respect to the Turner energy model for tiny (≈20 nt) RNA sequences ... binning structures into macrostates in a coarse-grained model, or by repeatedly simulating secondary structure...
  • PHAST

  • Referenced in 1 article [sw18806]
  • single or multiple heteropolymeric chains, as coarse-grained models for proteins. The outcome data...
  • SELM

  • Referenced in 3 articles [sw17574]
  • thermostats to extend implicit-solvent coarse-grained (IS-CG) models by incorporating kinetic contributions from ... Lagrangian method (SELM). SELM couples the coarse-grained microstructure degrees of freedom to continuum stochastic ... graphical user interface (GUI) for setting up models and simulations, (iv) standardized XML formats...
  • REACH

  • Referenced in 6 articles [sw00788]
  • program package for residue-scale coarse-grained biomolecular simulation. The program calculates the force constants ... residue-scale elastic network model in single-domain proteins using the variance–covariance matrix obtained ... atomistic simulation results onto a coarse-grained force field in an efficient automated procedure without...
  • ESPResSo++

  • Referenced in 3 articles [sw30328]
  • simulation and analysis of coarse-grained atomistic or bead-spring models as they are used...
  • MAVEN

  • Referenced in 2 articles [sw35124]
  • environment that automates many of the steps. Models can be constructed from raw PDB files ... atomic coordinates or by employing various coarse-graining procedures. Visualization can be performed either with ... exported to molecular viewers. Mixed resolution models allow one to study atomic effects ... computational speed of the coarse-grained ENMs. Analysis options are available to further...
  • QuakeTM

  • Referenced in 2 articles [sw09534]
  • task parallel model fits well. We provide a coarse-grained TM implementation characterized with eight...
  • downscale

  • Referenced in 1 article [sw37226]
  • measure for assessing its conservation status. Coarse-grained occupancy maps are available for many taxa ... atlases, but often at spatial resolutions too coarse for conservation use. However, mapping occupancy ... area occupied increases with spatial grain size. Models that describe the OAR are fitted ... available coarse-grain sizes and then extrapolated to predict occupancy at the finer grain sizes...
  • HiFlow3

  • Referenced in 8 articles [sw06354]
  • solution of a wide range of problems modeled by partial differential equations. Based on object ... systems – is introduced on two levels: coarse-grained parallelism by means of distributed grids...
  • LDEC

  • Referenced in 1 article [sw03262]
  • predict the coarse-grained fracture dynamics. Two approaches to modeling these phenomena are described...
  • Parkway

  • Referenced in 7 articles [sw12863]
  • partitioning tool. We recently proposed a coarse-grained parallel multilevel algorithm ... hypergraphs taken from the VLSI and performance modelling application domains. Further, partition quality in terms...
  • FlowDroid

  • Referenced in 5 articles [sw26741]
  • Android use a number of coarse-grain approximations that can yield high numbers of missed ... taint analysis for Android applications. A precise model of Android’s lifecycle allows the analysis...
  • STMBench7

  • Referenced in 9 articles [sw08814]
  • than explicit coarse-grained locking and easier to use than fine-grained locking. However ... collection of operations is supported to model a wide range of workloads and concurrency patterns...
  • HOOMD-TF

  • Referenced in 2 articles [sw40891]
  • calculation; EDS Biasing (See this paper); Coarse-Grained simulation force matching. In addition ... HOOMD-TF makes implementing arbitrary ML models as easy as it is in TensorFlow...
  • DistOpt

  • Referenced in 2 articles [sw01381]
  • DistOpt: A software framework for modeling and evaluating optimization problem solutions in distributed environments ... DistOpt, which is useful in building coarse-grain algorithms for solving optimization problems and simulating...
  • simpA

  • Referenced in 7 articles [sw00863]
  • context is to devise higher-level, coarse-grained abstractions that would help building concurrent programs ... formalizing the main aspects of this programming model...