Working Paper
Authors
- Fréderic Célerse Sorbonne University ,
- Theo Jaffrelot-Inizan Sorbonne University ,
- Louis Lagardère Sorbonne University ,
- Olivier Adjoua Sorbonne University ,
- Pierre Monmarché Sorbonne University ,
- Yinglong Miao University of Kansas ,
- Etienne Derat Sorbonne University ,
- Jean-Philip Piquemal
Sorbonne University
Abstract
We detail a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We then introduce the new "dual-water" mode and its use with the flexible AMOEBA polarizable force field.
By adding harmonic boosts to the water stretching and bonding terms, it accelerates the solvent-solute interactions while enabling speedups thanks to the use of fast multiple--timestep integrators. To further reduce time-to-solution, we couple GaMD to Umbrella Sampling (US). The GaMD—US/dual-water approach is tested on the 1D Potential of Mean Force (PMF) of the CD2-CD58 system (168000 atoms) allowing the AMOEBA PMF to converge within 1 kcal/mol of the experimental value. Finally, Adaptive Sampling (AS) is added enabling AS-GaMD capabilities but also the introduction of the new Adaptive Sampling--US--GaMD (ASUS--GaMD) scheme. The highly parallel ASUS--GaMD setup decreases time to convergence by respectively 10 and 20 compared to GaMD--US and US.
Version notes
Revised version.
Content

Supplementary material

Supplementary Materials
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