Development and application of enhanced sampling techniques to simulate the long-time scale dynamics of biomolecular systems

2011 ◽  
Vol 112 (1) ◽  
pp. 33-43 ◽  
Author(s):  
Justin Spiriti ◽  
Hiqmet Kamberaj ◽  
Arjan Van Der Vaart
Keyword(s):  
Time Scale ◽  
Sampling Techniques ◽  
Enhanced Sampling ◽  
Biomolecular Systems ◽  
Long Time

scholarly journals Towards Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Corrections

2021 ◽  
Author(s):  
Vojtech Mlynsky ◽  
Michal Janecek ◽  
Petra Kuhrova ◽  
Thorben Frohlking ◽  
Michal Otyepka ◽  
...  
Keyword(s):  
Time Scale ◽  
Md Simulations ◽  
Sampling Techniques ◽  
Enhanced Sampling ◽  
Free Energies ◽  
Native State ◽  
Good Convergence ◽  
Empirical Potentials ◽  
Folding Simulations ◽  
Established Technique

Atomistic molecular dynamics (MD) simulations represent established technique for investigation of RNA structural dynamics. Despite continuous development, contemporary RNA simulations still suffer from suboptimal accuracy of empirical potentials (force fields, ffs) and sampling limitations. Development of efficient enhanced sampling techniques is important for two reasons. First, they allow to overcome the sampling limitations and, second, they can be used to quantify ff imbalances provided they reach a sufficient convergence. Here, we study two RNA tetraloops (TLs), namely the GAGA and UUCG motifs. We perform extensive folding simulations and calculate folding free energies (ΔGfold) with the aim to compare different enhanced sampling techniques and to test several modifications of the nonbonded terms extending the AMBER OL3 RNA ff. We demonstrate that replica exchange solute tempering (REST2) simulations with 12-16 replicas do not show any sign of convergence even when extended to time scale of 120 μs per replica. However, combination of REST2 with well-tempered metadynamics (ST-MetaD) achieves good convergence on a time-scale of 5-10 μs per replica, improving the sampling efficiency by at least two orders of magnitude. Effects of ff modifications on ΔGfold energies were initially explored by the reweighting approach and then validated by new simulations. We tested several manually-prepared variants of gHBfix potential which improve stability of the native state of both TLs by up to ~2 kcal/mol. This is sufficient to conveniently stabilize the folded GAGA TL while the UUCG TL still remains under-stabilized. Appropriate adjustment of van der Waals parameters for C-H...O5' base-phosphate interaction are also shown to be capable of further stabilizing the native states of both TLs by ~0.6 kcal/mol.

scholarly journals Long-Time-Scale Magnetization Ordering Induced by an Adsorbed Chiral Monolayer on Ferromagnets

ACS Nano ◽  
2021 ◽  
Author(s):  
I. Meirzada ◽  
N. Sukenik ◽  
G. Haim ◽  
S. Yochelis ◽  
L. T. Baczewski ◽  
...  
Keyword(s):  
Time Scale ◽  
Long Time

scholarly journals Dynamics of transposable elements under the selection model

1999 ◽  
Vol 74 (2) ◽  
pp. 159-164 ◽  
Author(s):  
A. TSITRONE ◽  
S. CHARLES ◽  
C. BIÉMONT
Keyword(s):  
Equilibrium Point ◽  
Dynamic Characteristics ◽  
Time Scale ◽  
Copy Number ◽  
Stable Equilibrium ◽  
Stable Equilibrium Point ◽  
Asymptotically Stable ◽  
Weak Selection ◽  
Strong Selection ◽  
Long Time

We examine an analytical model of selection against the deleterious effects of transposable element (TE) insertions in Drosophila, focusing attention on the asymptotic and dynamic characteristics. With strong selection the only asymptotically stable equilibrium point corresponds to extinction of the TEs. With very weak selection a stable and realistic equilibrium point can be obtained. The dynamics of the system is fast for strong selection and slow, on the human time scale, for weak selection. Hence weak selection acts as a force that contributes to the stabilization of mean TE copy number. The consequence is that under weak selection, and ‘out-of-equilibrium’ situation can be maintained for a long time in populations, with mean TE copy number appearing stabilized.

scholarly journals Long Time Scale Dynamics of Molecules With Internal Rigid Fragments

2010 ◽  
Vol 98 (3) ◽  
pp. 27a
Author(s):  
Sebnem G. Essiz ◽  
Rob D. Coalson
Keyword(s):  
Time Scale ◽  
Long Time
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