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 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	= system	; 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

 

 

 

###npt.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	= system	; #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

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