Microstate sparse reconstruction, an optimization algorithm that solves the inverse problem: recovering an all-atom state consistent with a coarse-grained description.
Andrew Abi-Mansour
Department of Chemistry, Indiana University, Bloomington
ProtoMD - https://github.com/CTCNano/proto_md
PETSc - https://www.mcs.anl.gov/petsc
MDAnalysis - https://code.google.com/p/mdanalysis
Numpy - http://www.numpy.org
OpenMPI - http://www.open-mpi.org or MPICH - https://www.mpich.org
python MSRWriter.py struct traj tpr tol
-struct: structure file such as a pdb or gro file
-traj: trajectory file such as a trr, xtc, or dcd
-tpr: binary input file generated by Gromacs (with grompp) for reading topology
-tol: tolerance set for the atomic displacement, below convergence is assumed to be achieved