dorsal/arxiv
View SchemaThe Hierarchy of Fast Motions in Protein Dynamics
| Authors | Alexey K. Mazur |
|---|---|
| Categories | |
| ArXiv ID | physics/9801022 |
| URL | https://arxiv.org/abs/physics/9801022 |
| Journal | J. Phys. Chem. B (1998) 102(2), 473-479 |
Abstract
For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the system in order to increase the time step. An accurate knowledge of these motions is a necessary prerequisite for such efforts. It is known that harmonic vibrations of bond lengths and bond angles produce the highest frequencies in proteins. There are also fast anharmonic motions, such as inter-atomic collisions, which are probably most important when bond lengths and bond angles are fixed. However, the specific time scales corresponding to all these limitations are not known precisely. In order to clarify the above issue this paper analyses time step limiting factors in a series of numerical tests by using an internal coordinate molecular dynamics approach, which allows chosen internal coordinates to be frozen. It is found that, in proteins, there is a rather complicated hierarchy of fast motions, with both harmonic and anharmonic effects mixed together at several close time scales. Non-bonded interactions, notably strong hydrogen bonding, create locally distributed normal modes with frequencies similar to those of bond stretching between non-hydrogen atoms. They also impose ubiquitous anharmonic limitations starting from rather small step sizes. With fixed standard amino acid geometry, rotations of hydrogen bonded hydroxyl groups limit time steps at the 5 fsec level. The next important limitation occurs around 10 fsec and is created by collisions between non-hydrogen atoms.
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"abstract": "For many biological applications of molecular dynamics (MD) the importance of\ngood sampling in conformational space makes it necessary to eliminate the\nfastest motions from the system in order to increase the time step. An accurate\nknowledge of these motions is a necessary prerequisite for such efforts. It is\nknown that harmonic vibrations of bond lengths and bond angles produce the\nhighest frequencies in proteins. There are also fast anharmonic motions, such\nas inter-atomic collisions, which are probably most important when bond lengths\nand bond angles are fixed. However, the specific time scales corresponding to\nall these limitations are not known precisely. In order to clarify the above\nissue this paper analyses time step limiting factors in a series of numerical\ntests by using an internal coordinate molecular dynamics approach, which allows\nchosen internal coordinates to be frozen. It is found that, in proteins, there\nis a rather complicated hierarchy of fast motions, with both harmonic and\nanharmonic effects mixed together at several close time scales. Non-bonded\ninteractions, notably strong hydrogen bonding, create locally distributed\nnormal modes with frequencies similar to those of bond stretching between\nnon-hydrogen atoms. They also impose ubiquitous anharmonic limitations starting\nfrom rather small step sizes. With fixed standard amino acid geometry,\nrotations of hydrogen bonded hydroxyl groups limit time steps at the 5 fsec\nlevel. The next important limitation occurs around 10 fsec and is created by\ncollisions between non-hydrogen atoms.",
"arxiv_id": "physics/9801022",
"authors": [
"Alexey K. Mazur"
],
"categories": [
"physics.comp-ph",
"physics.bio-ph",
"physics.chem-ph",
"q-bio"
],
"journal_ref": "J. Phys. Chem. B (1998) 102(2), 473-479",
"title": "The Hierarchy of Fast Motions in Protein Dynamics",
"url": "https://arxiv.org/abs/physics/9801022"
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