Methods for Multiscale Modeling of Membranes

Goga, Nicolae; Rzepiela, Andrzej J.; Melo, Manuel N.; Vries, Alex de; Hadăr, Anton; Markvoort, Albert J.; Nedea, S.V.; Berendsen, Herman J. C.

doi:10.1016/b978-0-12-396533-2.00003-3

Cited by 6 publications

(8 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The average temperature and the standard error are computed using the formulas (12) and (13). Table 1 it can be noticed that when X is greater, meaning that there is more friction in the system, the best average temperatures are obtained for X = 100 on weakly and strongly coupled atoms, being the closest to the temperature taken as reference, that of 300 K. Obviously, the standard error has the lowest values for those cases.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Improved OpenMM algorithms for CUDA and OpenCL using new stochastic dynamics and the Berendsen thermostat

Moga

Marin

Goga

et al. 2015

2015 6th International Conference on Computing, Communication and Networking Technologies (ICCCNT)

View full text Add to dashboard Cite

The simulations done in molecular dynamics (MD) are used to learn about the behavior of macromolecular systems. While analyzing large macromolecular systems, the computation can last long, many times for days, weeks and months, due to which the need of parallelization occurs for shortening the time. The graphics processing unit (GPU) yields to multithread computational capacity by the use of CUDA high-level language which suits the molecular dynamics algorithms. The OpenCL platform allows its reckoning kernels to run without difficulty on GPUs, as well as on multicore computers. We developed a new thermostat that combines Langevin dynamics with the global Berendsen thermostat which is parallelized in CUDA, as well as in OpenCL. The GPU parallelization is presented in this paper by applying stochastic dynamics, respectively the Langevin integrator, together with the Berendsen thermostat. A system of atoms is tested by taking into consideration the friction coefficient and the coupling parameter.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Molecular dynamics [8,12,13], branch of bio informatics [17], has been conceived almost 60 years ago in theoretical physics and it is applied in chemical physics, materials science and in the modeling of molecules [6,14]. The aim of molecular dynamics is to simulate the changes which occur in a molecule as a function of time.…”

Section: Introductionmentioning

confidence: 99%

Improved OpenMM algorithms for CUDA and OpenCL using new stochastic dynamics and the Berendsen thermostat

Moga

Marin

Goga

et al. 2015

2015 6th International Conference on Computing, Communication and Networking Technologies (ICCCNT)

View full text Add to dashboard Cite

show abstract

“…When the friction is parallel to the interparticle distance (PAR), the unit vector is constructed, ij ij r r e = 1 (8) where r ij = r i -r j has to be constructed in the inter-particle direction. The vector which has the same orientation for friction, as well as for the velocity, v par = v * e 1 (9) Another from a standard normal distribution has to be chosen in order to construct the vector v, v = -(f * v par + g * ) * e 1 (10) The next step consists in the updating the velocity as in (15).…”

Section: Database and Methodsmentioning

confidence: 99%

Improved GROMACS algorithms using the MPI parallelization

Goga

Marin

Vasilățeanu

et al. 2015

2015 E-Health and Bioengineering Conference (EHB)

View full text Add to dashboard Cite

Molecular dynamics (MD) studies the structure of molecular systems which are subject to certain constraints and forces. The simulation of particles is a tool for examining atomic systems during a period of nanoseconds in which the trajectory of atoms and the state of the system is analyzed. GROMACS is a package which supports molecular dynamics simulations and energy minimization, being started the University of Groningen. Usually molecular dynamics simulations are time consuming, sometimes taking weeks and even months. In order to obtain the output of the simulation in less time, parallelization is used through the use of MPI (Message Passing Interface). The article presents the MPI parallelization of a novel thermostat algorithm for molecular dynamics and experimental results.

show abstract

“…Moreover, photoinduced water splitting requires treating excited states, which has been conventionally achieved with time-dependent DFT but is a distant challenge for large-scale simulations. The vision is that these nanoparticles must also be solvated and treated with an increased length scale …”

mentioning

confidence: 99%