Bernd Ensing

Bernd Ensing

Path-metadynamics with Plumed 2.5

Software to extend Plumed with path-metadynamics

Authors

Grisell Díaz Leines and Bernd Ensing

To use the path-metadynamics method [1] with Plumed download the PathCV.cpp file and save this file in your plumed-2 distribution in the directory src/function/PathCV.cpp. We are using Plumed version 2.5 at the moment). Secondly, add the following to the file in user-doc/bibliography.bib :

  @article{ensing12,

            Author = {Grisell Díaz Leines and Bernd Ensing},

            Journal = {Phys. Rev. Lett.},

            Month = {Feb},

            Pages = {020601},

           Title = {Path finding on high-dimensional free energy landscapes},

           Volume = {109},

           Year = {2012}}

After recompiling the code (make, make install, make doc) the documentation on how to use path-metadynamics is found in user-doc/html/index.html under Collective variables / Functions / PATHCV.

For a Plumed nest archive with example input files for path-metadynamics simulation of a proline tetramer with Plumed and Gromacs click on this link. Further instructions: This allows to run multiple-walker path-metadynamics on the right- to left-handed helix transition in tetrameric polyproline with a 3D CV-space. It can be easily adjusted to bigger systems with higher-dimensional CV-spaces. It requires PLUMED compiled with MPI and with the Path-CV code provided in the URL above. It also requires an MD engine that can run parallel replicas. We use GROMACS 5.1.4 compiled with MPI. Notice that in the PLUMED input files “WALKERS_ID” must be adjusted for the different walkers. This example is taken from the work published in Ref. [2].

plumID:19.033

References:

[1] Path finding on high-dimensional free energy landscapes. Grisell Díaz Leines and Bernd Ensing, Phys. Rev. Lett. 109 (2012), 020601 DOI: 10.1103/PhysRevLett.109.020601

[2] Advances in enhanced sampling along adaptive paths of collective variables. Alberto Pérez de Alba Ortíz , Ambuj Tiwari, Rakesh C. Puthenkalathil, and Bernd Ensing, J. Chem. Phys. 149 (2018), 072320 DOI: 10.1063/1.5027392

Path-metadynamics with Plumed 2.5