dorsal/arxiv
View SchemaUse of the Metropolis algorithm to simulate the dynamics of protein chains
| Authors | G. Tiana, L. Sutto, R. A. Broglia |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0606038 |
| URL | https://arxiv.org/abs/q-bio/0606038 |
| DOI | 10.1016/j.physa.2007.02.044 |
Abstract
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.
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"abstract": "The Metropolis implementation of the Monte Carlo algorithm has been developed\nto study the equilibrium thermodynamics of many-body systems. Choosing small\ntrial moves, the trajectories obtained applying this algorithm agree with those\nobtained by Langevin\u0027s dynamics. Applying this procedure to a simplified\nprotein model, it is possible to show that setting a threshold of 1 degree on\nthe movement of the dihedrals of the protein backbone in a single Monte Carlo\nstep, the mean quantities associated with the off-equilibrium dynamics (e.g.,\nenergy, RMSD, etc.) are well reproduced, while the good description of higher\nmoments requires smaller moves. An important result is that the time duration\nof a Monte Carlo step depends linearly on the temperature, something which\nshould be accounted for when doing simulations at different temperatures.",
"arxiv_id": "q-bio/0606038",
"authors": [
"G. Tiana",
"L. Sutto",
"R. A. Broglia"
],
"categories": [
"q-bio.OT"
],
"doi": "10.1016/j.physa.2007.02.044",
"title": "Use of the Metropolis algorithm to simulate the dynamics of protein chains",
"url": "https://arxiv.org/abs/q-bio/0606038"
},
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