9 papers
Computational Study of pKa shift of Aspartate residue in Thioredoxin: Role of Configurational Sampling and Solvent Model
Shivani Verma, Nisanth N. Nair
Alchemical free energy calculations are widely used in predicting pKa, and binding free energy calculations in biomolecular systems. These calculations are carried out using either…
Improving the Scaling and Performance of Multiple Time Stepping based Molecular Dynamics with Hybrid Density Functionals
Sagarmoy Mandal, Ritama Kar, Tobias Kloeffel +2
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) sim…
Boosting the Conformational Sampling by Combining Replica Exchange with Solute Tempering and Well-Sliced Metadynamics
Anji Babu Kapakayala, Nisanth N. Nair
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculatio…
Mean Force Based Temperature Accelerated Sliced Sampling: Efficient Reconstruction of High Dimensional Free Energy Landscapes
Asit Pal, Subhendu Pal, Shivani Verma +2
Temperature Accelerated Sliced Sampling (TASS) is an efficient method to compute high dimensional free energy landscapes. The original TASS method employs the Weighted Histogram An…
Achieving an Order of Magnitude Speed-up in Hybrid Functional and Plane Wave based Ab Initio Molecular Dynamics: Applications to Proton Transfer Reactions in Enzymes and in Solution
Sagarmoy Mandal, Vaishali Thakkur, Nisanth N. Nair
Ab initio molecular dynamics (AIMD) with hybrid density functionals and plane wave basis is computationally expensive due to the high computational cost of exact exchange energy ev…
Improving the Exploration of High Dimensional Free Energy Landscape by a Combination of Temperature Accelerated Sliced Sampling and Parallel Biasing
Abhinav Gupta, Shivani Verma, Nisanth N. Nair
Biased sampling methods such as the Temperature Accelerated Sliced Sampling (TASS), which can explore high dimensional collective variable (CV) space, is of great interest in free…