Project ID: plumID:23.003
Name: Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations
Archive: https://github.com/shirtsgroup/alchemical_metadynamics_project/archive/master.zip (browse)
Category: methods
Keywords: metadynamics, alchemical variable, alchemical free energy calculations
PLUMED version: 2.8
Contributor: Wei-Tse Hsu
Submitted on: 01 Feb 2023
Publication: W.-T. Hsu, V. Piomponi, P. T. Merz, G. Bussi, M. R. Shirts, Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations. Journal of Chemical Theory and Computation. 19, 1805–1817 (2023)

PLUMED input files

File Compatible with
Case_1/Test_1/1D_lambda_MetaD/rep_1/plumed.dat tested on v2.9 tested on master
…1/Test_1/1D_lambda_MetaD/rep_1/plumed_sum_bias.dat tested on v2.9 tested on master
Case_1/Test_1/1D_lambda_MetaD/rep_2/plumed.dat tested on v2.9 tested on master
…1/Test_1/1D_lambda_MetaD/rep_2/plumed_sum_bias.dat tested on v2.9 tested on master
Case_1/Test_1/1D_lambda_MetaD/rep_3/plumed.dat tested on v2.9 tested on master
…1/Test_1/1D_lambda_MetaD/rep_3/plumed_sum_bias.dat tested on v2.9 tested on master
Case_2/Prep/short_MD/MD/plumed_dihedral.dat tested on v2.9 tested on master
Case_2/Prep/torsion_MetaD/plumed.dat tested on v2.9 tested on master
…_2/Test_1/1D_lambda_MetaD/rep_1/State_A/plumed.dat tested on v2.9 tested on master
…/1D_lambda_MetaD/rep_1/State_A/plumed_dihedral.dat tested on v2.9 tested on master
…/1D_lambda_MetaD/rep_1/State_A/plumed_sum_bias.dat tested on v2.9 tested on master
…_2/Test_1/1D_lambda_MetaD/rep_1/State_B/plumed.dat tested on v2.9 tested on master
…/1D_lambda_MetaD/rep_1/State_B/plumed_dihedral.dat tested on v2.9 tested on master
…/1D_lambda_MetaD/rep_1/State_B/plumed_sum_bias.dat tested on v2.9 tested on master
…_2/Test_1/1D_lambda_MetaD/rep_2/State_A/plumed.dat tested on v2.9 tested on master
…/1D_lambda_MetaD/rep_2/State_A/plumed_dihedral.dat tested on v2.9 tested on master
…/1D_lambda_MetaD/rep_2/State_A/plumed_sum_bias.dat tested on v2.9 tested on master
…_2/Test_1/1D_lambda_MetaD/rep_2/State_B/plumed.dat tested on v2.9 tested on master
…/1D_lambda_MetaD/rep_2/State_B/plumed_dihedral.dat tested on v2.9 tested on master
…/1D_lambda_MetaD/rep_2/State_B/plumed_sum_bias.dat tested on v2.9 tested on master

Last tested: 26 Feb 2024, 07:17:33

Project description and instructions
The method of alchemical metadynamics has been implemented in PLUMED 2.8, which can be used when PLUMED is patched to any GROMACS version later than 2020. All simulation inputs, including input GRO, TOP, TPR, and PLUMED input files have been provided for each case presented in our paper, along with relevant python codes and jupyter notebook for data analysis. More information can be found in the README files in the repo.

Submission history
[v1] 01 Feb 2023: original submission

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