Software DLPROTEIN | EGI Applications Database

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Name:DLPROTEIN

Description:DLPROTEIN is a package to simulate complex molecular environments. Molecular Dynamics is the key physical method to reproduce the atomic motion at high accuracy. A suite of software utilities assist the user in designing and handling the molecular topologies and analysing the output of the simulations. The package has several branches and options in order to
- Build and Manage complex structures starting from crystallographic data
- Use popular force fields (Charmm, Gromos, Amber) as well as add/modify new ones
- Simulate large systems with high efficiency and low memory requirements
- Use a large combination of potential functions
- Allow fast and accurate electrostatics (Coulomb, Ewald, SMPE, etc.)
- Use various boundary conditions (vacuo, parallelepiped, octahedron, dodecahedron)
- Perform Parallel and Scalar runs on several platforms
- Use either Single or Multiple Time Step propagation algorithms
- Sample various Statistical Ensembles
- Use bond and conic constraints
- Analyse structures with biological software tools
DLPROTEIN is distributed as free software and Open Source. An extensive documentation accompanies the package

Software requirements: Fortran compilers, standard math libraries, MPICH libraries, FFTW libraries^

Abstract:DLPROTEIN is a package to simulate complex molecular environments. Molecular Dynamics is the key physical method to reproduce the atomic motion at high accuracy. A suite of software utilities assist the user in designing and handling the molecular topologies and analysing the output of the simulations. The package has several branches and options in order to - Build and Manage complex structures starting from crystallographic data - Use popular force fields (Charmm, Gromos, Amber) as well as add/modify new ones - Simulate large systems with high efficiency and low memory requirements - Use a large combination of potential functions - Allow fast and accurate electrostatics (Coulomb, Ewald, SMPE, etc.) - Use various boundary conditions (vacuo, parallelepiped, octahedron, dodecahedron) - Perform Parallel and Scalar runs on several platforms - Use either Single or Multiple Time Step propagation algorithms - Sample various Statistical Ensembles - Use bond and conic constraints - Analyse structures with biological software tools DLPROTEIN is distributed as free software and Open Source. An extensive documentation accompanies the package Software requirements: Fortran compilers, standard math libraries, MPICH libraries, FFTW libraries^