Gromacs

Core MD modules

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    This is a list of planned core MD modules, dealing mainly with force calculation and integration, i.e. the internals of mdrun.

     

    • Name:    Interaction Evaluation
      Descr:   Calculates interactions for a microstate
      Depen:   Bonded int., Non-bonded int.
      Input:   Rules, Microstate, Switches
      Output:  V, F and/or virial
      Req:     Maximum efficiency, will use cache
       
    • Name:    Bonded/Listed Interaction Evaluation
      Descr:   Calculates interactions from a specified list (in the rules)
      Depen:  
      Input:   Rules, Microstate, Switches
      Output:  V, F and/or virial, evaluation count (for checking the total count)
      Req:     Maximum efficiency, will use cache (e.g. force tables)
       
    • Name:    Bonded/Listed Interaction Evaluation
      Descr:   Calculates interactions from a specified list (in the rules)
      Depen:  
      Input:   Rules, Microstate, Switches
      Output:  V, F and/or virial, evaluation count (for checking the total count)
      Req:     Maximum efficiency, will use cache (e.g. force tables)
       
    • Name:    Pair Interaction Evaluation
      Descr:   Calculates pair interactions within a cut-off distance
      Depen:  
      Input:   Rules, Microstate, Switches
      Output:  V, F and/or virial
      Req:     Maximum efficiency, will use cache (e.g. pair list, force tables)
       
    • Name:    Virtual Sites
      Descr:   Determines virtual site coordinates and redistribute forces
      Depen:  
      Input:   Rules, Microstate or F
      Output:  Microstate or F
      Req:     Could cache coefficients from X calculation for F
       
    • Name:    Propagation
      Descr:   Propagates the microstate with several MD, EM or MC propagators
      Depen:   Constraints
      Input:   Microstate, F, T, P, Hamiltonian state, external fields
      Output:  V, F and/or virial
      Req:     Should support several integrators using a few hooks
       
    • Name:    Constraints
      Descr:   Applies contraints to unconstrained X, V or F
      Depen:  
      Input:   Rules, Microstate and possibly F
      Output:  Constrained (or constraint components of) X, V or F
      Req:     Must be able to work in parallel with MPI and/or threads
       
    • Name:    Measurements
      Descr:   Handles measurements during simulation
      Depen:   I/O
      Input:   Microstate, Energies, ...
      Output:  Energy file, Log
      Req:     Also records history which needs to be stored in checkpoint
       
    • Name:    Energy Reduction (separate from Measurements?)
      Descr:   Reduce local energy terms over MPI processes (and threads?)
      Depen:  
      Input:   Local energies
      Output:  Global energies
      Req:    
       
    • Name:    Domain Decomposition
      Descr:   Decomposes the system over domains and handles communication
      Depen:  
      Input:   Global Rules, Global Microstate, Parallel system setup
      Output:  Local Rules, Local Microstate
      Req:    
       
    • Name:  COM calculation
      Descr:  Calculates center of mass(es) of group(s) of particles
      Depen:
      Input:  Coordinate and mass vector distributed over processes/threads, group(s)
      Output: COM(s) on each thread/process
      Req:
    Page last modified 03:30, 26 May 2011 by Michael Shirts