Parallelizing a Molecular Dynamics Algorithm on a Multiprocessor Workstation Using OpenMP

Abstract

The atomistic molecular dynamics program YASP has been parallelized for shared-memory computer architectures. Parallelization was restricted to the most CPU-time-consuming parts: neighbor-list construction, calculation of nonbonded, angle and dihedral forces, and constraints. Most of the sequential FORTRAN code was kept; parallel constructs were inserted as compiler directives using the OpenMP standard. Only in the case of the neighbor list did the data structure have to be changed. The parallel code achieves a useful speedup over the sequential version for systems of several thousand atoms and above. On an IBM Regatta p690+, the throughput increases with the number of processors up to a maximum of 12-16 processors depending on the characteristics of the simulated systems. On dual-processor Xeon systems, the speedup is about 1.7.

Properties of Polyvinyl Alcohol Oligomers: A Molecular Dynamics Study

“…Afterward we have carried out a set of MD simulations of 200 ps each by using soft-core potentials as implemented in our simulation package YASP. [21][22][23] This allows the atoms to pass through each other and guarantees that the whole system gets rid of possible entanglements. The strain is thereby minimized.…”

“…The strain is thereby minimized. We have performed eight relaxation simulations starting with the potential energy V 0 ¼ 0.3 k B T at zero atom-atom distance [21][22][23] and ending with V 0 ¼ 60 k B T before using the full non-bonded potential. The six intermediate V 0 parameters chosen amount to 1.5, 6, 12, 24, 36, and 48 k B T. This step was followed by a relaxation simulation of the oligomer bulk at a constant temperature of 400 K and a constant pressure of 101.3 kPa until the total energy and the mass density reached their equilibrium values.…”

“…[21][22][23] The temperature and pressure were kept constant using the Berendsen thermostat and barostat [24] with coupling times of 0.2 and 3.0 ps, respectively.…”

Correlation between thermal conductivity and bond length alternation in carbon nanotubes: A combined reverse nonequilibrium molecular dynamics—Crystal orbital analysis

“…The RNE method has been implemented into the MD code YASP. 73,74 All RNEMD simulations of this study have been performed with it.…”

A comparison of sulfur mustard and heptane penetrating a dipalmitoylphosphatidylcholine bilayer membrane

“…The simulation package which was chosen for this investigation is YASP, which was initially written by Müller-Plathe [20] and has recently been parallelized by Tarmyshov and Müller-Plathe [21].…”