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

本仓库说明

本仓库针对肝素与淀粉样β肽(16-22)的自组装模拟，设置了多组变量参数，包括肽链数目（N_pep）、肝素分子数（N_hep）、肝素聚合度（hep_dp）以及肝素刚性因子（rig_f）。本仓库为每个模拟体系单独创建一个文件夹，每个文件夹由四个体系变量（N_pep、N_hep、hep_dp及rig_f）的组合唯一标识。

本模拟基于GROMACS 2019.4分子动力学引擎完成，采用ProMPT力场进行粗粒度分子动力学（coarse-grained molecular dynamics）模拟。每个体系均开展四次独立重复模拟（trial_A、trial_B、trial_C及trial_D），各模拟采用不同的初始速度，单轮模拟时长为3000纳秒（ns）。

### 仓库内容
> heparin_abeta_trajectories.zip
本仓库包含压缩包heparin_abeta_trajectories.zip，其内包含13个按规范命名的文件夹，命名格式为`{N_pep}pep_{N_hep}hep_dp{hep_dp}_{rig_f}xRigid`。例如，包含16条肽链（N_pep）、1个肝素分子（N_hep）、聚合度为18的肝素链（hep_dp）且刚性因子为100（rig_f）的体系，其数据将存储于目录`16pep_1hep_dp18_100xRigid/`中。

若体系不含肝素，则默认将N_hep、hep_dp及rig_f设为0。例如，仅包含16条肽链（N_pep）且无肝素的体系，其数据将存储于目录`16pep_0hep_dp0_0xRigid/`中。

以目录`16pep_1hep_dp18_100xRigid/`为例，其内部包含以下文件与子目录：

solute_only.ndx：仅包含溶质分子（肽链和/或肝素）的索引组文件。

trial_A/：
- md.tpr：用于生成当前轨迹的可移植运行文件，可用于复现该模拟轨迹。
- solute_only.cluster_center.xtc：仅包含溶质分子（肽链和/或肝素）的GROMACS轨迹文件，通过GROMACS工具gmx trjconv完成轨迹居中对齐处理。
- solute_only.tpr：仅包含溶质分子（肽链和/或肝素）数据的GROMACS可移植二进制输入文件，通过gmx convert-tpr工具生成，可用于分析`solute_only.cluster_center.xtc`轨迹。

trial_B/、trial_C/及trial_D/：内部文件与trial_A/完全一致。

> psf_files_for_VMD_visualization.zip
本压缩包包含13个.psf格式文件，每个文件对应一个模拟体系，可与`solute_only.cluster_center.xtc`轨迹文件配合，用于在可视化分子动力学软件（Visual Molecular Dynamics, VMD）中展示模拟轨迹。

如需获取本模拟轨迹的核心背景信息，请查阅相关发表学术论文。
如需获取模拟搭建的原始文件及简要教程，请访问：https://github.com/suhasgotla/heparin_amyloid_self-assembly