Use of the Metropolis algorithm to simulate the dynamics of protein chains

Details Use of the Metropolis algorithm to simulate the dynamics of protein chains Use of the Metropolis algorithm to simulate the dynamics of protein chains

2006-06-27

arxiv.org/abs/q-bio/0606038v2

Biology

Quantitative Biology

Other Quantitative Biology

corrections to the text and to the figures

Scientific paper

10.1016/j.physa.2007.02.044

The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those obtained by Langevin's dynamics. Applying this procedure to a simplified protein model, it is possible to show that setting a threshold of 1 degree on the movement of the dihedrals of the protein backbone in a single Monte Carlo step, the mean quantities associated with the off-equilibrium dynamics (e.g., energy, RMSD, etc.) are well reproduced, while the good description of higher moments requires smaller moves. An important result is that the time duration of a Monte Carlo step depends linearly on the temperature, something which should be accounted for when doing simulations at different temperatures.

Affiliated with

Also associated with

No associations

Rating

Use of the Metropolis algorithm to simulate the dynamics of protein chains does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Use of the Metropolis algorithm to simulate the dynamics of protein chains, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Use of the Metropolis algorithm to simulate the dynamics of protein chains will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-572553