  Molecular dynamics facilitates the simulation of a complex system to be
analyzed at molecular and atomic levels. Simulations can last a long period of
time, even months. Due to this cause the graphics processing units (GPUs) and
multi-core systems are used as solutions to overcome this impediment. The
current paper describes a comparison done between these two kinds of systems.
The first system used implies the graphics processing unit, respectively CUDA
with the OpenMM molecular dynamics package and OpenCL that allows the kernels
to run on the GPU. This simulation is done on a new thermostat which mixes the
Berendsen thermostat with the Langevin dynamics. The second comprises the
molecular dynamics simulation and energy minimization package GROMACS which is
based on a parallelization through MPI (Message Passing Interface) on
multi-core systems. The second simulation uses another new thermostat algorithm
related respectively, dissipative particle dynamics - isotropic type (DPD-ISO).
Both thermostats are innovative, based on a new theory developed by us. Results
show that parallelization on multi-core systems has a performance up to 33
times greater than the one performed on the graphics processing unit. In both
cases temperature of the system was maintained close to the one taken as
reference. For the simulation using the CUDA GPU, the faster runtime was
obtained when the number of processors was equal to four, the simulation speed
being 3.67 times faster compared to the case of only one processor.
