Project ID: plumID:23.018
Name: Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention
Archive: https://github.com/katorke/Au_Facet_Selectivity/raw/main/plumed_nest.zip
Category: materials
Keywords: metadynamics, surface binding, peptide adsorption
PLUMED version: 2.8
Contributor: Kaylyn Torkelson
Submitted on: 11 May 2023
Publication: K. J. Lachowski, H. T. Chiang, K. Torkelson, W. Zhou, S. Zhang, J. Pfaendtner, L. D. Pozzo, Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention. Langmuir. 39, 15878–15888 (2023)

PLUMED input files

File Compatible with
Z2M246I_Au100/plumed.dat tested on v2.9 tested on master
Z2M246I_Au111/plumed.dat tested on v2.9 tested on master
Z2_Au100/plumed.dat tested on v2.9 tested on master
Z2_Au111/plumed.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:47:58

Project description and instructions
Each directory (Z2_Au100, Z2_Au111, Z2M246I_Au100, Z2M246I_Au111) contains an initial gro file (system.gro) for the system, a corresponding index file (system.ndx), a reference PDB for each peptide, the files necessary for the topology of the system (topol.top/*.itp), and the plumed file (plumed.dat) that was used to run each metadynamics calculation in Gromacs 2020.5. The main directory contains an example MDP file, the forcefield that was used for Au interactions, and the ndx files corresponding to the Au(111) and Au(100) surfaces.

Submission history
[v1] 11 May 2023: original submission

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plumeDnest:23.018