Molecular dynamics trajectories and portable binary run files for the self-assembly of heparin and amyloid-β(16-22) with the ProMPT forcefield

About this repository Self-assembly simulations of heparin and amyloid-β(16-22) were performed at various numbers of peptides (N_pep), number of heparin molecules (N_hep), degrees of polymerization of heparin (hep_dp) and rigidity factors (rig_f) for heparin. This repository contains one folder per system, characterized by a combination of four system variables: N_pep, N_hep, hep_dp and rig_f. The simulations were performed on the GROMACS 2019.4 molecular dynamics engine, with the ProMPT forcefield for coarse-grained molecular dynamics. Four independent trials: trial_A, trial_B, trial_C and trial_D were performed per system, each with different starting velocities. Each trial was run for 3000 ns. Contents > heparin_abeta_trajectories.zip The repository contains the zip file heparin_abeta_trajectories.zip with 13 folders named according to the convention, "{N_pep}pep_{N_hep}hep_dp{hep_dp}_{rig_f}xRigid". For example, data for the system consisting of 16 peptides (N_pep), 1 heparin (N_hep), 18 monosaccharides in length (hep_dp) with a rigidity factor of 100 (rig_f) would be stored in the directory 16pep_1hep_dp18_100xRigid/. If the system did not contain heparin, N_hep, hep_dp and rig_f were set to 0 by default. For example, data for the system consisting of 16 peptides (N_pep) and no heparin would be stored in the directory 16pep_0hep_dp0_0xRigid/. A directory such as 16pep_1hep_dp18_100xRigid/ will have the following contents: solute_only.ndxContains an index group for solute molecules (peptides and/or heparin) only. trial_A/ md.tpr Portable run file with which the current trajectory was generated. This file may be used to reproduce the trajectory as well. solute_only.cluster_center.xtc A gromacs trajectory containing only the solute molecules (peptides and/or heparin), centered with the gromacs tool gmx trjconv solute_only.tpr A gromacs portable binary input file containing data for the solute molecules (peptides and/or heparin) only, generated with the gmx convert-tpr tool.This file may be used during analysis of the solute_only.cluster_center.xtc trajectory. trial_B/contents same as trial_A/ trial_C/contents same as trial_A/ trial_D/contents same as trial_A/ > psf_files_for_VMD_visualization.zip This zip file contains thirteen .psf files, one per system, that can be used in accord with solute_only.cluster_center.xtc files to visualize trajectories on the Visual Molecular Dynamics (VMD) software. Please seek out the associated publication for essential context on these trajectories. To access the source files with which these simulations were set-up, and a brief tutorial, see: https://github.com/suhasgotla/heparin_amyloid_self-assembly