Project ID: plumID:23.023
Name: Rational design of novel biomimetic sequence-defined polymers for mineralization applications
Archive: https://github.com/katorke/R5_Mineralization/raw/main/plumed_nest.zip
Category: methods
Keywords: metadynamics, surface binding, biomimetic mineralization
PLUMED version: 2.8
Contributor: Kaylyn Torkelson
Submitted on: 15 Jun 2023
Publication: K. Torkelson, N. Y. Naser, X. Qi, Z. Li, W. Yang, K. Pushpavanam, C.-L. Chen, F. Baneyx, J. Pfaendtner, Rational Design of Novel Biomimetic Sequence-Defined Polymers for Mineralization Applications. Chemistry of Materials. 36, 786–794 (2024)
PLUMED input files
| File | Compatible with |
|---|---|
| dimer_files/plumed.dat |   |
| silicate_files/plumed.dat | |
| surface_files/plumed.dat | |
Last tested: 22 Apr 2025, 10:01:07
Project description and instructions
Each directory (dimer_files, silicate_files, surface_files) contains an example gro file (system.gro), the topology files needed to run that system (*.itp and topol.top), an example mdp file, and the plumed.dat file corresponding to each simulation type. Each metadynamics calculation was run in GROMACS 2020.5 with PLUMED 2.8. The main directory contains a directory named PDB that has example structures for all five systems studied (R5 peptide, R5 peptoid mimic, R5 peptoid analog, R5 peptide reverse, and R5 peptoid analog reverse) as well as another forcefield directory that contains all the modifications necessary to run our peptoid systems.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 15 Jun 2023: original submission
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