An improved replica-exchange sampling method: Temperature intervals with global energy reassignment

2007 ◽  
Vol 127 (16) ◽  
pp. 164116 ◽  
Author(s):  
Xianfeng Li ◽  
Christopher P. O’Brien ◽  
Galen Collier ◽  
Nadeem A. Vellore ◽  
Feng Wang ◽  
...  
Keyword(s):  
Sampling Method ◽  
Replica Exchange ◽  
Global Energy

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 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.

A novel ligand with –NH2 and –COOH-decorated Co/Fe-based oxide for an efficient overall water splitting: dual modulation roles of active sites and local electronic structure

2020 ◽  
Vol 10 (18) ◽  
pp. 6266-6273
Author(s):  
Yalan Zhang ◽  
Zebin Yu ◽  
Ronghua Jiang ◽  
Jung Huang ◽  
Yanping Hou ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Water Splitting ◽  
Energy Demand ◽  
Active Sites ◽  
Electrode Materials ◽  
Global Energy ◽  
Overall Water Splitting ◽  
Local Electronic Structure ◽  
Electrochemical Water Splitting

Excellent electrochemical water splitting with remarkable durability can provide a solution to satisfy the increasing global energy demand in which the electrode materials play an important role.

An Empirical Analysis of the Obtrusiveness of and Participants' Compliance with the Electronically Activated Recorder (EAR)

2007 ◽  
Vol 23 (4) ◽  
pp. 248-257 ◽  
Author(s):  
Matthias R. Mehl ◽  
Shannon E. Holleran
Keyword(s):  
Empirical Analysis ◽  
Sampling Method ◽  
Daily Life ◽  
Assessment Method ◽  
Data Confidentiality ◽  
Short Term ◽  
Naturally Occurring ◽  
Two Samples ◽  
Audio Recorder ◽  
Term Monitoring

Abstract. In this article, the authors provide an empirical analysis of the obtrusiveness of and participants' compliance with a relatively new psychological ambulatory assessment method, called the electronically activated recorder or EAR. The EAR is a modified portable audio-recorder that periodically records snippets of ambient sounds from participants' daily environments. In tracking moment-to-moment ambient sounds, the EAR yields an acoustic log of a person's day as it unfolds. As a naturalistic observation sampling method, it provides an observer's account of daily life and is optimized for the assessment of audible aspects of participants' naturally-occurring social behaviors and interactions. Measures of self-reported and behaviorally-assessed EAR obtrusiveness and compliance were analyzed in two samples. After an initial 2-h period of relative obtrusiveness, participants habituated to wearing the EAR and perceived it as fairly unobtrusive both in a short-term (2 days, N = 96) and a longer-term (10-11 days, N = 11) monitoring. Compliance with the method was high both during the short-term and longer-term monitoring. Somewhat reduced compliance was identified over the weekend; this effect appears to be specific to student populations. Important privacy and data confidentiality considerations around the EAR method are discussed.

Emotional Variability Predicts Tiredness in Daily Life

2016 ◽  
Vol 37 (3) ◽  
pp. 181-193 ◽  
Author(s):  
Aire Mill ◽  
Anu Realo ◽  
Jüri Allik
Keyword(s):  
Sampling Method ◽  
Daily Life ◽  
Emotional Experience ◽  
Experience Sampling ◽  
Experience Sampling Method ◽  
Building Blocks ◽  
Intraindividual Variability ◽  
Unique Role ◽  
Over Time

Abstract. Intraindividual variability, along with the more frequently studied between-person variability, has been argued to be one of the basic building blocks of emotional experience. The aim of the current study is to examine whether intraindividual variability in affect predicts tiredness in daily life. Intraindividual variability in affect was studied with the experience sampling method in a group of 110 participants (aged between 19 and 84 years) during 14 consecutive days on seven randomly determined occasions per day. The results suggest that affect variability is a stable construct over time and situations. Our findings also demonstrate that intraindividual variability in affect has a unique role in predicting increased levels of tiredness at the momentary level as well at the level of individuals.

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