Dataset Information

Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant.

ABSTRACT: The replica-exchange molecular dynamics (REMD) method has been used for conformational sampling of various biomolecular systems. To maximize sampling efficiency, some adjustable parameters must be optimized. Although it is agreed that shorter intervals between the replica-exchange attempts enhance traversals in the temperature space, details regarding the artifacts caused by these short intervals are controversial. In this study, we revisit this problem by performing REMD simulations on an alanine octapeptide in an implicit solvent. Fifty different sets of conditions, which are a combination of five replica-exchange periods, five different numbers of replicas, and two thermostat coupling time constants, were investigated. As a result, although short replica-exchange intervals enhanced the traversals in the temperature space, they led to artifacts in the ensemble average of the temperature, potential energy, and helix content. With extremely short replica-exchange intervals, i.e., attempted at every time step, the ensemble average of the temperature deviated from the thermostat temperature by ca. 7 K. Differences in the ensembles were observed even for larger replica-exchange intervals (between 100 and 1,000 steps). In addition, the shorter thermostat coupling time constant reduced the artifacts found when short replica-exchange intervals were used, implying that these artifacts are caused by insufficient thermal relaxation between the replica-exchange events. Our results will be useful to reduce the artifacts found in REMD simulations by adjusting some key parameters.

SUBMITTER: Iwai R

PROVIDER: S-EPMC6145944 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Levan has various potential applications in the pharmaceutical and food industries, such as cholesterol-lowering agents and prebiotics, due to its beneficial properties, which depend on its length and branching degree. A previous study also found that the branching degree of levan affected anti-tumor activities against SNU-1 and HepG2 tumor cell lines. Despite its promising potential, the properties of levans with different branching degrees are not well understood at the molecular level. In two models of the generalized Born implicit solvent (GBHCT and GBOBC1), we employed replica-exchange molecular dynamics simulations to explore conformational spaces of 34-residue levans (L34) with branching degrees of zero (LFO34B0), one (LFO34B1), three (LFO34B3) and five (LFO34B5), as well as to elucidate their structural and molecular properties. To ensure a fair comparison of the effects of branching degree on these properties, we focused on analyzing the properties of the central 21-residue of the main chains of all systems. Our results show that all major representative conformations tend to form helix-like structures with kinks, where two-kink helix-like structures have the highest population. As branching degree increases, the population of helix-like structures with zero or one kink tends to increase slightly. As the number of kinks in the structures with the same branching degree increases, the average values of the lengths and angles among centers of masses of three consecutive turns of residue i, i+3, and i+6 tended to decrease. Due to its highest occurring frequencies, the O6 (i)-H3O (i+1) hydrogen bond could be important for helix-like structure formation. Moreover, hydrogen bonds forming among the branching residue (br), branching position (bp) and other residues of L34B1, L34B3 and L34B5 were identified. The O1(bp)-H3O(br), O1(br)-H3O(br) and O5(br)-H1O(br) hydrogen bonds were found in the first-, second- and third-highest occurrence frequencies, respectively. Our study provides novel and important insights into conformational spaces and the structural and molecular properties of 34-residue levans with various branching degrees, which tend to form helix-like structures with kinks.

Dataset Information

Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets