Coordinates scaling and multiple time step algorithms for simulation of solvated proteins in the NPT ensemble

Constant pressure and temperature algorithms have been derived based on a reversible multiple time step (r-RESPA) approach and a new modification of the particle mesh Ewald method. As such they provide very fast and accurate tools for simulation of complex molecular systems in ensembles other than the microcanonical. We have also developed a novel scaling scheme named atomic group scaling which is similar to atomic scaling, but has important computational advantages when used in conjunction with bond constraints. The investigation of the molecular and atomic group scaling schemes against static and dynamic properties of a test system (a solvated bovine pancreatic trypsin inhibitor) has confirmed their equivalence also for large molecules such as proteins. For the specific test system the simulation box cell volume upon changes of pressure decays to its equilibrium value within 5 ps of simulation for both approaches. This goes against theoretical arguments that molecular scaling would not be suitable for s...

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