GROMACS运行参数之em.mdp文件详解

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添加离子过程中需要用到输入文件em.mdp，现对里面的各种编辑项目做简单注释。

###em.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= system; 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

###npt.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= system; #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