Simulated annealing coupled replica exchange molecular dynamics—An efficient conformational sampling method

2009 ◽  
Vol 166 (3) ◽  
pp. 288-294 ◽  
Author(s):  
Srinivasaraghavan Kannan ◽  
Martin Zacharias
Keyword(s):  
Molecular Dynamics ◽  
Simulated Annealing ◽  
Sampling Method ◽  
Replica Exchange ◽  
Conformational Sampling ◽  
Replica Exchange Molecular Dynamics

scholarly journals Exploring Protocols to Build Reservoirs to Accelerate Replica Exchange MD Simulations

2020 ◽  
Author(s):  
koushik kasavajhala ◽  
kenneth lam ◽  
Carlos Simmerling
Keyword(s):  
Amino Acids ◽  
Sampling Method ◽  
Convergence Rates ◽  
Md Simulations ◽  
Replica Exchange ◽  
Conformational Sampling ◽  
Enhanced Sampling ◽  
Replica Exchange Molecular Dynamics ◽  
The Past ◽  
Biomolecular Simulations

Replica Exchange Molecular Dynamics (REMD) is a widely used enhanced sampling method for accelerating biomolecular simulations. During the past two decades, several variants of REMD have been developed to further improve the rate of conformational sampling of REMD. One such variant, Reservoir REMD (RREMD), was shown to improve the rate of conformational sampling by around 5-20x. Despite the significant increase in sampling speed, RREMD methods have not been widely used due to the difficulties in building the reservoir and also due to the code not being available on the GPUs.<br><br>In this work, we ported the AMBER RREMD code onto GPUs making it 20x faster than the CPU code. Then, we explored protocols for building Boltzmann-weighted reservoirs as well as non-Boltzmann reservoirs, and tested how each choice affects the accuracy of the resulting RREMD simulations. We show that, using the recommended protocols outlined here, RREMD simulations can accurately reproduce Boltzmann-weighted ensembles obtained by much more expensive conventional REMD simulations, with at least 15x faster convergence rates even for larger proteins (>50 amino acids) compared to conventional REMD.

scholarly journals Multiscale implementation of infinite-swap replica exchange molecular dynamics

2016 ◽  
Vol 113 (42) ◽  
pp. 11744-11749 ◽  
Author(s):  
Tang-Qing Yu ◽  
Jianfeng Lu ◽  
Cameron F. Abrams ◽  
Eric Vanden-Eijnden
Keyword(s):  
Molecular Dynamics ◽  
Joint Distribution ◽  
Jump Process ◽  
Stochastic Simulation Algorithm ◽  
Replica Exchange ◽  
Conformational Sampling ◽  
Markov Jump ◽  
Replica Exchange Molecular Dynamics ◽  
Different Temperatures ◽  
Heterogeneous Multiscale

Replica exchange molecular dynamics (REMD) is a popular method to accelerate conformational sampling of complex molecular systems. The idea is to run several replicas of the system in parallel at different temperatures that are swapped periodically. These swaps are typically attempted every few MD steps and accepted or rejected according to a Metropolis–Hastings criterion. This guarantees that the joint distribution of the composite system of replicas is the normalized sum of the symmetrized product of the canonical distributions of these replicas at the different temperatures. Here we propose a different implementation of REMD in which (i) the swaps obey a continuous-time Markov jump process implemented via Gillespie’s stochastic simulation algorithm (SSA), which also samples exactly the aforementioned joint distribution and has the advantage of being rejection free, and (ii) this REMD-SSA is combined with the heterogeneous multiscale method to accelerate the rate of the swaps and reach the so-called infinite-swap limit that is known to optimize sampling efficiency. The method is easy to implement and can be trivially parallelized. Here we illustrate its accuracy and efficiency on the examples of alanine dipeptide in vacuum and C-terminal β-hairpin of protein G in explicit solvent. In this latter example, our results indicate that the landscape of the protein is a triple funnel with two folded structures and one misfolded structure that are stabilized by H-bonds.

scholarly journals Exploring Protocols to Build Reservoirs to Accelerate Replica Exchange MD Simulations

2020 ◽  
Author(s):  
koushik kasavajhala ◽  
kenneth lam ◽  
Carlos Simmerling
Keyword(s):  
Amino Acids ◽  
Sampling Method ◽  
Convergence Rates ◽  
Md Simulations ◽  
Replica Exchange ◽  
Conformational Sampling ◽  
Enhanced Sampling ◽  
Replica Exchange Molecular Dynamics ◽  
The Past ◽  
Biomolecular Simulations

Replica Exchange Molecular Dynamics (REMD) is a widely used enhanced sampling method for accelerating biomolecular simulations. During the past two decades, several variants of REMD have been developed to further improve the rate of conformational sampling of REMD. One such variant, Reservoir REMD (RREMD), was shown to improve the rate of conformational sampling by around 5-20x. Despite the significant increase in sampling speed, RREMD methods have not been widely used due to the difficulties in building the reservoir and also due to the code not being available on the GPUs.<br><br>In this work, we ported the AMBER RREMD code onto GPUs making it 20x faster than the CPU code. Then, we explored protocols for building Boltzmann-weighted reservoirs as well as non-Boltzmann reservoirs, and tested how each choice affects the accuracy of the resulting RREMD simulations. We show that, using the recommended protocols outlined here, RREMD simulations can accurately reproduce Boltzmann-weighted ensembles obtained by much more expensive conventional REMD simulations, with at least 15x faster convergence rates even for larger proteins (>50 amino acids) compared to conventional REMD.

Solution Study of Engineered Quartz Binding Peptides Using Replica Exchange Molecular Dynamics

2010 ◽  
Vol 11 (12) ◽  
pp. 3266-3274 ◽  
Author(s):  
Rebecca Notman ◽  
E. Emre Oren ◽  
Candan Tamerler ◽  
Mehmet Sarikaya ◽  
Ram Samudrala ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Solution Study ◽  
Binding Peptides
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