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Nanoscale Molecular Dynamics

Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer software for molecular dynamics simulation, written… 
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AbaloneBiochemical and Organic Simulation SystemC++CHARMM

Papers overview

Semantic Scholar uses AI to extract papers important to this topic.
2017
2017
ACCELERATING PROTEIN CONFORMATIONAL SAMPLING USING MULTISCALE APPROACH
Searching conformational ensembles of proteins remains a challenge in atomistic simulation of biomolecules. One approach to… 
2016
2016
Handling Transient and Persistent Imbalance Together in Distributed and Shared Memory
  • 2016
  • Corpus ID: 1619070
The recent trend of rapid increase in the number of cores per chip has resulted in vast amount of on-node parallelism. Not only… 
2015
2015
Identification of potent VEGFR-2 Inhibitors of Angiogenesis through homology modeling, Structure based virtual screening, docking and molecular dynamics simulations
VEGFR-2 is a known protein target for antiangiogenic agents, was used in this study. In order to understand of the mechanisms of… 
2011
2011
Synthetic and natural Zn-Al sulphate LDHs for removal of As(V) from NAMD
2011
2011
Considerations and Recent Advances in Molecular Dynamics
  • S. Ye
  • 2011
  • Corpus ID: 6658317
Molecular dynamics simulations were first proposed in the 1950-60s as a method to study the motions of atoms at the molecular… 
2008
2008
Implementation of NAMD molecular dynamics non-bonded force-field on the cell broadband engine processor
We present results of porting an important kernel of a production molecular dynamics simulation program, NAMD, to the Cell/B.E… 
2008
2008
AnAdaptiveSynchronizationTechniquefor P arallelSimulationofNetworkedClusters
Computer clusters are a very cost–effective approach for High Performance Computing, but simulating a complete cluster is still… 
2008
2008
Pretty Fast Analysis: An embarrassingly parallel algorithm for biological simulation analysis
A parallel code has been written in FORTRAN90, C, and MPI for the analysis of biological simulation data. Using a master/slave… 
2006
2006
An Investigation of Simultaneous Multithreading on HPCx
The use of Simultaneous Multithreading (SMT) on HPCx is investigated to determine if any performance improvement is obtainable… 
1998
1998
Avoiding Algorithmic Obfuscation in a Message-driven Parallel Md Code
Parallel molecular dynamics programs employing shared memory or replicated data architectures encounter problems scaling to large… 
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