Nedelcu, R.-A., Caramihai, S.I., Goga, N., and Stanescu, A.M.
2015 6th International Conference on Computing, Communication and Networking Technologies (ICCCNT) Computing, Communication and Networking Technologies (ICCCNT), 2015 6th International Conference on. :1-5 Jul, 2015
Vasilateanu, A., Goga, N., Sutu, T., Moldoveanu, A., Asavei, V., and Taslitchi, C.
2013 19th International Conference on Control Systems and Computer Science International Conference on Control Systems and Computer Science Control Systems and Computer Science (CSCS), 2013 19th International Conference on. :263-267 May, 2013
Canadian Conference on Electrical and Computer Engineering 2004 (IEEE Cat. No.04CH37513) Electrical and computer engineering Electrical and Computer Engineering, 2004. Canadian Conference on. 2:673-676 Vol.2 2004
2004 IEEE International Conference on Systems, Man and Cybernetics (IEEE Cat. No.04CH37583) Systems, man and cybernetics Systems, Man and Cybernetics, 2004 IEEE International Conference on. 6:5154-5158 vol.6 2004
Goga, N., Rzepiela, A. J., de Vries, A. H., Marrink, S. J., and Berendsen, H. J. C.
Journal of Chemical Theory and Computation; October 2012, Vol. 8 Issue: 10 p3637-3649, 13p
In this article, we present several algorithms for stochastic dynamics, including Langevin dynamics and different variants of Dissipative Particle Dynamics (DPD), applicable to systems with or without constraints. The algorithms are based on the impulsive application of friction and noise, thus avoiding the computational complexity of algorithms that apply continuous friction and noise. Simulation results on thermostat strength and diffusion properties for ideal gas, coarse-grained (MARTINI) water, and constrained atomic (SPC/E) water systems are discussed. We show that the measured thermal relaxation rates agree well with theoretical predictions. The influence of various parameters on the diffusion coefficient is discussed.
Goga, N., Melo, M. N., Rzepiela, A. J., de Vries, A. H., Hadar, A., Marrink, S. J., and Berendsen, H. J. C.
Journal of Chemical Theory and Computation; April 2015, Vol. 11 Issue: 4 p1389-1398, 10p
In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications namely those of sampling enhancement it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hybrid approach with an adjustable mixing parameter. We present a benchmark of three algorithms that use a mixing of the two representation layers using a Lagrangian formalism. The three algorithms use three different approaches for keeping the particles at the FG level of representation together: 1) addition of forces, 2) mass scaling, and 3) temperature scaling. The benchmark is applied to liquid hexadecane and includes an evaluation of the average configurational entropy of the FG and CG subsystems. The temperature-scaling scheme achieved a 3-fold sampling speedup with little deviation of FG properties. The addition-of-forces scheme kept FG properties the best but provided little sampling speedup. The mass-scaling scheme yielded a 5-fold speedup but deviated the most from FG properties.
Peters, E. A. J. F., Goga, N., and Berendsen, H. J. C.
Journal of Chemical Theory and Computation; October 2014, Vol. 10 Issue: 10 p4208-4220, 13p
In this paper we discuss thermostatting using stochastic methods for molecular simulations where constraints are present. For so-called impulsive thermostats, like the Andersen thermostat, the equilibrium temperature will differ significantly from the imposed temperature when a limited number of particles are picked and constraints are applied. We analyze this problem and give two rigorous solutions for it. A correct general treatment of impulsive stochastic thermostatting, including pairwise dissipative particle dynamics and stochastic forcing in the presence of constraints, is given and it is shown that the constrained canonical distribution is sampled rigorously. We discuss implementation issues such as second order Trotter expansions. The method is shown to rigorously maintain the correct temperature for the case of extended simple point charge (SPC/E) water simulations.