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  • Last update: 5 years ago
  • Total downloads: 64
  • Operating system: WinXP, Win2000, Win Vista, Windows 7, Windows 8
  • Publisher: ProtoMol Team
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windows default iconProtoMol Publisher's description

ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations.

ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. The framework supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The technique of multiple time-stepping is used to improve long-term efficiency. The use of fast electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME), and Multigrid (MG) summation further enhances performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators.


An object-oriented component based framework for molecular dynamics simulations
Designed for high flexibility, easy extendibility and maintenance, and high performance demands
Incremental parallelization combining sequential and parallel environment
Support of generic multiple time-stepping integration schemes
Generic forces and potentials
Fast electrostatic force evaluation algorithms:

Ewald summation, O(N3/2)
Particle-Mesh-Ewald, O(N log N)
Multi-grid method, O(N)

Support of common I/O formats (pre- & post-processing)
106 particle systems

What's New in This Release:

В· Added integrator that numerically differentiates the hessian using a five-point center difference method and computes error with respect to analytical hessian. Updated Normal Mode Diagonalize to use geometric fixed dof and numerical small Hessian and S calculation.
В· Updated protomol to allow usage of Intel's Math Kernel Library
В· Deterministic ordering in passing random values to vectors in Langevin derivative methods.
В· Fix to allow compiling with visual studio on a 64bit system
В· Updated report so that it is possible to set 'debugstart' this then prints debug output from 'debugstart' (default 0) to 'debug' for greater diagnostic granularity.
В· Added numerical Hessian code. HessianInt has two new parameters to select the geometric fixed degrees of freedom and numerical Hessian calculation. The code has been regression tested in the 'non geometric and numerical' mode. Added XTC writer. Requires gromacs 4.5+ library (gromacs=1 and set GROMACS_HOME), keyword 'XTCfile'.
В· Added TPR reader to...

System Requirements:

No special requirements.
Program Release Status: New Release
Program Install Support: Install and Uninstall

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