Project ID: plumID:21.010
Name: Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry
Archive: https://github.com/physix-repo/glycine_strecker_plumed/raw/main/supplementary_files_archives.zip
Category: chemistry
Keywords: Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis
PLUMED version: 1.3
Contributor: Théo Magrino
Submitted on: 08 Mar 2021
Publication: T. Magrino, F. Pietrucci, A. M. Saitta, Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry. The Journal of Physical Chemistry Letters. 12, 2630–2637 (2021)

PLUMED input files

File Compatible with
umbrella-sampling_1-2prime/g1-w1-s1.308/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w10-s3.252/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w11-s3.468/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w12-s3.684/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w13-s3.900/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w14-s4.116/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w15-s4.332/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w16-s4.548/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w17-s4.764/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w18-s4.980/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w19-s5.196/plumed.dat tested on v2.8 tested on master
umbrella-sampling_1-2prime/g1-w2-s1.524/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w20-s5.412/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w21-s5.628/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w22-s5.844/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w23-s6.060/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w24-s6.276/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w25-s6.492/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w26-s6.708/plumed.dat tested on v2.8 tested on master
…mbrella-sampling_1-2prime/g1-w27-s6.924/plumed.dat tested on v2.8 tested on master

Last tested: 19 Nov 2022, 10:50:18

Project description and instructions
Supplementary files for this article. The files available here are necessary for reproducing work. Files MTD_X-Y_plumed.dat and MTD_X-Y_frames.dat contain respectively input files for PLUMED 1.3 and corresponding reference structures for path-based CVs definition. Files MTD_X-Y_plumed.dat and MTD_X-Y_frames.dat correspond to metadynamics that allows exploration between metastable states X and Y. Folders umbrella_sampling_X-Y contain each a serie of folders that correspond to umbrella sampling windows. Each folder contains plumed.dat and frames.dat input for plumed1.3. Umbrella sampling between metastable states X and Y is made of the comprehensive set of simulations contains in the umbrella_sampling_X-Y.

Submission history
[v1] 08 Mar 2021: original submission

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