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Running biased simulations with PLUMED and ACEMD

Toni Giorgino, 2019

National Research Council of Italy

This is a test case reproducing the phi-psi alanine dipeptide free energy plot shown e.g. in [1] via a metadynamics-biased simulation. We use ACEMD. [3] The current version, ACEMD3, supports PLUMED 2 [4]. Input files are provided in the corresponding subdirectories of this repository.

For information, tutorial and documentation about PLUMED see http://www.plumed.org/.

Methods

This demo computes the phi-psi free energy landscape of the alanine dipeptide via well-tempered metadynamics [1]. The dipeptide is modelled in vacuo with the CHARMM forcefield. The total length of the run is 10 ns, simulated with a timestep of 1 fs. There are 100,000 gaussians in total, deposited at a rate of 1 every 100 fs.

Installation

This demo relies on PLUMED 2 and ACEMD3 version >=3.3.0. The easiest way to obtain them is to install the corresponding packages through Acellera's conda channel, which includes the required ACEMD-compatible version of PLUMED packaged as a shared library. If you installed acemd via Conda, you may already have it in your system.

Reconstruction of the free energy landscape

Reconstruction of the free energy landscape occurs post-processing the HILLS files via the sum_hills utility. For PLUMED 1 it is a separate utility, while for PLUMED 2 it is invoked via plumed sum_hills. So,

shell> plumed sum_hills --hills HILLS   # PLUMED2

generates a fes.dat file which can be plotted as follows:

gnuplot> plot 'fes.dat' with image

Notes:

  • You can try "sum_hills" then "gnuplot" even while the simulation is running. This allows you to see metadynamics in action, gradually filling the free energy surface.
  • The animation files in the reference directories show an illustration of what's happening. There are 1000 animation frames taken at 10 ps intervals. Between each frame and the next, 100 gaussians are deposited. Observe how (at the beginning) the free energy basins are alternatively filled.

Metadynamics parameters

These are set in META_INP or plumed.dat, respectively. (The files can be renamed; here we used the "traditional" names.)

  • CV1: Torsion between atoms 13 15 17 1
  • CV2: Torsion between atoms 15 17 1 3
  • Hill width 0.2 Å on both CVs
  • Hill height 0.1 kcal/mol/rad², deposition rate 1/100 fs (10 per ps)
  • Well-tempered metadynamics at T=300°K and bias factor 10.

References

[1] A Laio and F L Gervasio. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep. Prog. Phys. 71 (2008) doi:10.1088/0034-4885/71/12/126601

[2] M Bonomi et al, PLUMED: a portable plugin for free-energy calculations with molecular dynamics. arXiv:0902.0874v3

[3] M. Harvey, G. Giupponi and G. De Fabritiis, ACEMD: Accelerated molecular dynamics simulations in the microseconds timescale, J. Chem. Theory and Comput. 5, 1632 (2009).

[4] Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi, Carlo Camilloni, Giovanni Bussi, PLUMED 2: New feathers for an old bird, Computer Physics Communications, Volume 185, Issue 2, 2014, Pages 604-613, ISSN 0010-4655, http://dx.doi.org/10.1016/j.cpc.2013.09.018.

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