MD simulation of 50-lipid DOPS monolayers in the water-air interface, CHARMM36+OPC4[+1/80] @298.15K

This record contains the simulation files of 50-lipid DOPS monolayers simulated in the water-air interface without counterions. It models the situation when experimentator doesn't have any electrolyte in the solution but DOPS is still deprotonated by some reason (which is probably not the case, because DOPS is likely almost completely protonated at these conditions).

The initial strcuture of the systems was assembled using CHARMM-GUI, with sodium counterions to neutralize the system, and equilibrated with GROMACS v.2024.x by following their recommended protocol. Then sodium ions where removed and their charge were distributed over all water molecules (adding +0.0125 to every MW particle of OPC4). Then the monolayer were equilibrated at zero sufrace tension, and then the membrane was then compressed and expanded in a simulation using PLUMED, from which states at different values of area per lipid (APL) were extracted.

Each of these systems was the initial state of a 100 ns long simulation in the NVT ensemble (T=298.15 K), the ones here provided.

For all simulations, CHARMM36 parameters for the lipids and the 4-point OPC water model were used.

Files provided:

Compressed file with all ITP files with the parameters used for the simulations.

MDP file used for the production simulations.

For each simulation, TOP with the topology, TRR of the simulation, trajectory in TRR format, energy contributions in EDR format,  CPT generated and GRO with the final state of the system. All files corresponding to the same simulation are labeled as NVT_XX, where XX is the nominal APL at which the simulations were carried out.

本数据集包含含50个脂质分子的DOPS单分子层在水-气界面（无抗衡离子）条件下的模拟文件。该模型模拟了实验者未在溶液中添加任何电解质，但DOPS因某种原因仍处于去质子化状态的场景（注：实际该场景大概率不成立，因为在此条件下DOPS几乎完全质子化）。

体系初始结构通过CHARMM-GUI组装，初始采用钠离子抗衡离子中和体系，并遵循官方推荐流程借助GROMACS v.2024.x版本完成平衡模拟。随后移除体系内的钠离子，并将其电荷分配至所有水分子：为每个OPC4水模型的氧原子（MW粒子）添加+0.0125的电荷。接着将单分子层在零表面张力下完成平衡，随后借助PLUMED开展膜的压缩与扩张模拟，从中提取出不同单位脂质面积（Area Per Lipid, APL）下的体系状态。

本数据集提供的每个体系均为时长100 ns的NVT系综（温度T=298.15 K）模拟的初始状态，即本次发布的所有体系。所有模拟均采用脂质的CHARMM36力场参数与四点水模型OPC4。

提供的文件包括：
1. 包含所有模拟所用参数的ITP文件压缩包；
2. 生产模拟所用的MDP文件；
3. 针对每个模拟，分别提供拓扑文件TOP、TRR格式的模拟轨迹文件、EDR格式的能量贡献文件、生成的CPT文件，以及体系最终状态的GRO文件。同一模拟的所有文件均以NVT_XX命名，其中XX为该模拟对应的标称单位脂质面积（APL）数值。