GROMACS(5.1.4)教程：蛋白质配体复合物
官网：点击打开链接
李老师博客：点击打开链接
蛋白质配体复合物模拟能量最小化过程中需要用到输入文件em_real.mdp，现对里面的各种编辑项目做简单注释。
###em_real.mdp###
; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform energygrps = Protein JZ4 ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions
中文注释仅供参考
###em_real.mdp###
; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; Parameters describing what to do, when to stop and what to save integrator = steep ; #指定积分算法 emtol = 1000.0 ; #能量最小化收敛值 emstep = 0.01 ; #初试步长 nsteps = 50000 ; #积分或能量最小化步数 energygrps = Protein JZ4 ; 保存能量的组 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; #邻近列表更新频率 cutoff-scheme = Verlet ns_type = grid ; #邻近列表搜索方法 rlist = 1.0 ; #短程邻近列表截断，默认1nm coulombtype = PME ; #库伦计算方式 rcoulomb = 1.0 ; #短程库伦截断，默认1nm rvdw = 1.0 ; #短程范德华力截断，默认1nm pbc = xyz ; #周期性边界条件
