Simulations of POPC bilayers and monolayers at three different sizes. CHARMM36 with OPC, TIP3P, and TIPS3P water models with modified masses

Simulations of POPC bilayers and monolayers with the CHARMM36 force field and mass-scaled standard TIP3P, CHARMM-specific TIP3P ("TIPS3P"), and OPC water models. These water models have approximately equal viscosities. Three system sizes are used: small ("S", 64 lipids), medium ("M", 256 lipids), and large ("L", 1024 lipids). All simulations are 1 µs long. The simulations are performed using GROMACS, and for each system the following are provided for bilayers ("BIL") and monolayers ("MONO"):

run input file (tpr)

energy file (edr)

trajectory file (xtc)

checkpoint file (cpt) 

final structure (gro)

Additionally, the following are shared by the monolayer and bilayer:

index file (ndx)

topology file (top)

The simulation parameter files (mdp) are provided separately for bilayers and monolayers. The molecular topologies (top) are included in TOP.tar.

The TIPS3P data are available in version 2.

The CHARMM36 force field is obtained from http://mackerell.umaryland.edu/charmm_ff.shtml

本数据集包含采用CHARMM36力场（CHARMM36 force field），结合质量缩放型标准TIP3P、CHARMM专属TIPS3P（TIPS3P）以及OPC水模型的POPC双层膜与单层膜模拟体系。上述三类水模型的黏度近似相等。本次模拟设置三种体系规模：小型（"S"，含64个脂质分子）、中型（"M"，含256个脂质分子）与大型（"L"，含1024个脂质分子），所有模拟时长均为1 µs。

本模拟采用GROMACS软件完成，针对双层膜（"BIL"）与单层膜（"MONO"）体系，分别提供以下文件：
1. 运行输入文件（tpr格式）
2. 能量文件（edr格式）
3. 轨迹文件（xtc格式）
4. 检查点文件（cpt格式）
5. 最终结构文件（gro格式）

此外，单层膜与双层膜体系共享以下文件：
1. 索引文件（ndx格式）
2. 拓扑文件（top格式）

模拟参数文件（mdp格式）单独为双层膜与单层膜体系分别提供。分子拓扑文件（top格式）打包于TOP.tar压缩包中。

TIPS3P相关数据收录于版本2中。CHARMM36力场可从http://mackerell.umaryland.edu/charmm_ff.shtml 获取。