scholarly journals ExTASY: Scalable and flexible coupling of MD simulations and advanced sampling techniques

Author(s):  
Vivekanandan Balasubramanian ◽  
Iain Bethune ◽  
Ardita Shkurti ◽  
Elena Breitmoser ◽  
Eugen Hruska ◽  
...  
2013 ◽  
Author(s):  
Josep Arnó ◽  
Michael Frunzi ◽  
Chris Weber ◽  
Dustin Levy

2015 ◽  
Vol 112 (27) ◽  
pp. 8181-8186 ◽  
Author(s):  
Richard C. Remsing ◽  
Erte Xi ◽  
Srivathsan Vembanur ◽  
Sumit Sharma ◽  
Pablo G. Debenedetti ◽  
...  

Liquid water can become metastable with respect to its vapor in hydrophobic confinement. The resulting dewetting transitions are often impeded by large kinetic barriers. According to macroscopic theory, such barriers arise from the free energy required to nucleate a critical vapor tube that spans the region between two hydrophobic surfaces—tubes with smaller radii collapse, whereas larger ones grow to dry the entire confined region. Using extensive molecular simulations of water between two nanoscopic hydrophobic surfaces, in conjunction with advanced sampling techniques, here we show that for intersurface separations that thermodynamically favor dewetting, the barrier to dewetting does not correspond to the formation of a (classical) critical vapor tube. Instead, it corresponds to an abrupt transition from an isolated cavity adjacent to one of the confining surfaces to a gap-spanning vapor tube that is already larger than the critical vapor tube anticipated by macroscopic theory. Correspondingly, the barrier to dewetting is also smaller than the classical expectation. We show that the peculiar nature of water density fluctuations adjacent to extended hydrophobic surfaces—namely, the enhanced likelihood of observing low-density fluctuations relative to Gaussian statistics—facilitates this nonclassical behavior. By stabilizing isolated cavities relative to vapor tubes, enhanced water density fluctuations thus stabilize novel pathways, which circumvent the classical barriers and offer diminished resistance to dewetting. Our results thus suggest a key role for fluctuations in speeding up the kinetics of numerous phenomena ranging from Cassie–Wenzel transitions on superhydrophobic surfaces, to hydrophobically driven biomolecular folding and assembly.


2020 ◽  
Author(s):  
Sebastian Wingbermühle ◽  
Lars V. Schäfer

Enhanced sampling techniques are a promising approach to obtain reliable binding free energy profiles for flexible protein-ligand complexes from molecular dynamics (MD) simulations. To put four popular enhanced sampling techniques to a biologically relevant and challenging test, we studied the partial dissociation of an antigenic peptide from the Major Histocompatibility Complex I (MHC I) HLA-B*35:01 to systematically investigate the performance of Umbrella Sampling (US), Replica Exchange with Solute Tempering 2 (REST2), Bias Exchange Umbrella Sampling (BEUS, or replica-exchange umbrella sampling), and well-tempered Metadynamics (MTD). With regard to the speed of sampling and convergence, the peptide-MHC I complex (pMHC I) under study showcases intrinsic strengths and weaknesses of the four enhanced sampling techniques used. We found that BEUS can handle best the sampling challenges that arise from the coexistence of an enthalpically and an entropically stabilized free energy minimum in the pMHC I under study. These findings might be relevant also for other flexible biomolecular systems with competing enthalpically and entropically stabilized minima.<br>


Electronics ◽  
2018 ◽  
Vol 7 (10) ◽  
pp. 257 ◽  
Author(s):  
Marco Migliore

The aim of this review paper is to discuss some of the advanced sampling techniques proposed in the last decade in the framework of planar near-field measurements, clarifying the theoretical basis of the different techniques, and showing the advantages in terms of number of measurements. Instead of discussing the details of the techniques, the attention is focused on their theoretical bases to give a gentle introduction to the techniques. For each sampling method, examples on a liner array are discussed to clarify the advantages and disadvantages of the method.


2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Marco Govoni ◽  
Jonathan Whitmer ◽  
Juan de Pablo ◽  
Francois Gygi ◽  
Giulia Galli

AbstractThe functionality of many materials is critically dependent on the integration of dissimilar components and on the interfaces that arise between them. The description of such heterogeneous components requires the development and deployment of first principles methods, coupled to appropriate dynamical descriptions of matter and advanced sampling techniques, in order to capture all the relevant length and time scales of importance to the materials’ performance. It is thus essential to build simple, streamlined computational schemes for the prediction and design of multiple properties of broad classes of materials, by developing interoperable codes which can be efficiently coupled to each other to perform complex tasks. We discuss the use of interoperable codes to simulate the structural and spectroscopic characterization of materials, including chemical reactions for catalysis, the description of defects for quantum information science, and heat and charge transport.


2020 ◽  
Author(s):  
Rajeswari Appadurai ◽  
Jayashree Nagesh ◽  
Anand Srivastava

AbstractDetermining the conformational ensemble for proteins with multi-funneled complex free-energy landscapes is often not possible with classical structure-biology methods that produce time and ensemble averaged data. With vastly improved force fields and advances in rare-event sampling methods, molecular dynamics (MD) simulations offer a complementary approach towards determining the collection of 3-dimensional structures that proteins can adopt. However, in general, MD simulations need to either impose restraints or reweigh the generated data to match experiments. The limitations extend beyond systems with high free-energy barriers as is the case with metamorphic proteins such as RFA-H. The predicted structures in even weakly-funneled intrinsically disordered proteins (IDPs) such as Histatin-5 (His-5) are too compact relative to experiments. Here, we employ a new computationally-efficient parallel-tempering based advanced-sampling method applicable across proteins with extremely diverse free-energy landscapes. And we show that the calculated ensemble averages match reasonably well with the NMR, SAXS and other biophysical experiments without the need to reweigh. We benchmark our method against standard model systems such as alanine di-peptide, TRP-cage and β-hairpin and demonstrate significant enhancement in the sampling efficiency. The method successfully scales to large metamorphic proteins such as RFA-H and to highly disordered IDPs such as His-5 and produces experimentally-consistent ensemble. By allowing accurate sampling across diverse landscapes, the method enables for ensemble conformational sampling of deep multi-funneled metamorphic proteins as well as highly flexible IDPs with shallow multi-funneled free-energy landscape.Significance/Authors’ SummaryGenerating high-resolution ensemble of intrinsically disordered proteins, particularly the highly flexible ones with high-charge and low-hydrophobicity and with shallow multi-funneled free-energy landscape, is a daunting task and often not possible since information from biophysical experiments provide time and ensemble average data at low resolutions. At the other end of the spectrum are the metamorphic proteins with multiple deep funnels and elucidating the structures of the transition intermediates between the fold topologies is a non-trivial exercise. In this work, we propose a new parallel-tempering based advanced-sampling method where the Hamiltonian is designed to allow faster decay of water orientation dynamics, which in turn facilitates accurate and efficient sampling across a wide variety of free-energy landscapes.


2020 ◽  
Author(s):  
Sebastian Wingbermühle ◽  
Lars V. Schäfer

Enhanced sampling techniques are a promising approach to obtain reliable binding free energy profiles for flexible protein-ligand complexes from molecular dynamics (MD) simulations. To put four popular enhanced sampling techniques to a biologically relevant and challenging test, we studied the partial dissociation of an antigenic peptide from the Major Histocompatibility Complex I (MHC I) HLA-B*35:01 to systematically investigate the performance of Umbrella Sampling (US), Replica Exchange with Solute Tempering 2 (REST2), Bias Exchange Umbrella Sampling (BEUS, or replica-exchange umbrella sampling), and well-tempered Metadynamics (MTD). With regard to the speed of sampling and convergence, the peptide-MHC I complex (pMHC I) under study showcases systematic strengths and weaknesses of the four enhanced sampling techniques used, demonstrating that BEUS can handle best the enthalpic and entropic sampling challenges posed by the system. We expect these findings to be relevant also for other flexible protein-ligand complexes with competing enthalpically and entropically stabilized minima.<br>


2020 ◽  
Author(s):  
Sebastian Wingbermühle ◽  
Lars V. Schäfer

Enhanced sampling techniques are a promising approach to obtain reliable binding free energy profiles for flexible protein-ligand complexes from molecular dynamics (MD) simulations. To put four popular enhanced sampling techniques to a biologically relevant and challenging test, we studied the partial dissociation of an antigenic peptide from the Major Histocompatibility Complex I (MHC I) HLA-B*35:01 to systematically investigate the performance of Umbrella Sampling (US), Replica Exchange with Solute Tempering 2 (REST2), Bias Exchange Umbrella Sampling (BEUS, or replica-exchange umbrella sampling), and well-tempered Metadynamics (MTD). With regard to the speed of sampling and convergence, the peptide-MHC I complex (pMHC I) under study showcases intrinsic strengths and weaknesses of the four enhanced sampling techniques used. We found that BEUS can handle best the sampling challenges that arise from the coexistence of an enthalpically and an entropically stabilized free energy minimum in the pMHC I under study. These findings might be relevant also for other flexible biomolecular systems with competing enthalpically and entropically stabilized minima.<br>


2004 ◽  
Vol 126 (49) ◽  
pp. 16038-16047 ◽  
Author(s):  
Jianhan Chen ◽  
Wonpil Im ◽  
Charles L. Brooks

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