GROMACS运行参数之em_real.mdp文件详解
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GROMACS(5.1.4)教程:蛋白质配体复合物
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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 COMMENTStitle= Minimization; Title of run; Parameters describing what to do, when to stop and what to saveintegrator= steep; Algorithm (steep = steepest descent minimization)emtol= 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/molemstep = 0.01 ; Energy step sizensteps= 50000 ; Maximum number of (minimization) steps to performenergygrps= 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 interactionsnstlist = 1 ; Frequency to update the neighbor list and long range forcescutoff-scheme = Verletns_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 interactionsrcoulomb = 1.0; long range electrostatic cut-offrvdw = 1.0; long range Van der Waals cut-offpbc = xyz ; Periodic Boundary Conditions中文注释仅供参考
###em_real.mdp###
; LINES STARTING WITH ';' ARE COMMENTStitle= Minimization; Title of run; Parameters describing what to do, when to stop and what to saveintegrator= 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 interactionsnstlist = 1 ; #邻近列表更新频率cutoff-scheme = Verletns_type = grid; #邻近列表搜索方法rlist = 1.0; #短程邻近列表截断,默认1nmcoulombtype = PME; #库伦计算方式rcoulomb = 1.0; #短程库伦截断,默认1nmrvdw = 1.0; #短程范德华力截断,默认1nmpbc = xyz ; #周期性边界条件
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