Force Field Parameters

These are MD trajectories to accompany the paper: "Lipid Binding and Force Transduction in MscL: A Continuum-Molecular Approach" by Juan M. Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be read and analyzed by the standard GROMACS utilities. Trajectories (.xtc) can also be visualized by common molecular graphics programs such as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and binary (.tpr) form are included, as well as simulation parameters (.mdp). In some cases text files (.xvg) including coordinate information are also included. The file MscL_Equilibration.tar.gz contains the trajectory corresponding to the 500 ns equilibration period of the MscL Channel embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz contains the trajectories for the tensionless and tensioned simulations, as well as the files needed to visualize the traction on the surface of the protein. The stress tensor was calculated with a custom version of GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be visualized with the program ParaView. The file Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation trajectories used to estimate the strength of lipid binding to the MscL protein. The file Channel_Actuation.tar.gz contains the steered MD simulation trajectories used to actuate the MscL channel by pulling on protein-bound lipids. Finally, the file force_field_parameters.tar.gz contains the parameters used in all of the simulations. We used the G43A1-S3 lipid parameters in combination with the G54A7 protein parameters.本数据集为配套于Juan M. Vanegas与Marino Arroyo于2014年发表于《PLoS ONE》的论文《脂质结合与MscL中的力转导：一种连续介质-分子方法》的分子动力学（MD）轨迹文件。所有轨迹均通过GROMACS 4.5.5版本（www.gromacs.org）生成。标准GROMACS工具即可读取并分析所有轨迹。轨迹文件（.xtc格式）还可通过UCSF Chimera（http://www.cgl.ucsf.edu/chimera/）或VMD（http://www.ks.uiuc.edu/Research/vmd/）等常用分子可视化程序进行可视化。 数据集包含文本格式（.top）与二进制格式（.tpr）的拓扑文件，以及模拟参数文件（.mdp）。部分场景下还附带了包含坐标信息的文本文件（.xvg）。 具体压缩包内容如下： 1. MscL_Equilibration.tar.gz：包含嵌入POPE双分子层的MscL通道500 ns平衡阶段的轨迹文件。 2. Local_Stress_and_Traction.tar.gz：包含无张力与有张力模拟的轨迹，以及用于可视化蛋白表面牵引力所需的文件。应力张量通过定制版GROMACS（http://www.lacan.upc.edu/LocalStressFromMD）计算，相关文件可通过ParaView程序可视化。 3. Arrhenius_Bell_unbinding.tar.gz：包含用于估算脂质与MscL蛋白结合强度的拉伸分子动力学（steered MD）模拟轨迹。 4. Channel_Actuation.tar.gz：包含通过牵拉结合于蛋白的脂质以激活MscL通道的拉伸分子动力学模拟轨迹。 5. force_field_parameters.tar.gz：包含所有模拟所使用的力场参数。本次模拟采用G43A1-S3脂质参数与G54A7蛋白参数组合。