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md运行过程中需要用到输入文件md.mdp,现对里面的各种编辑项目做简单注释。
###md.mdp###
title = Protein-ligand complex MD simulation
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress .trr output
nstvout = 0 ; suppress .trr output
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; write .xtc trajectory every 10.0 ps
compressed-x-grps = System
energygrps = Protein JZ4
; Bond parameters
continuation = yes ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_JZ4 Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; assign velocities from Maxwell distribution
中文注释仅供参考
###md.mdp###
title = Protein-ligand complex MD simulation
; Run parameters
integrator = md ; #指定积分算法;md:蛙跳牛顿积分算法,用于平衡动力学积分
nsteps = 500000 ; #积分或能量最小化步数
dt = 0.002 ; #积分步长
; Output control
nstxout = 0 ; #坐标保存到轨迹文件的频率
nstvout = 0 ; #速度保存到轨迹文件的频率
nstenergy = 5000 ; #能量保存到轨迹文件的频率,必须是nstcalcenergy的倍数
nstlog = 5000 ; # log文件更新频率
nstxout-compressed = 5000 ; #
compressed-x-grps = System
energygrps = Protein JZ4 #保存能量的组
; Bond parameters
continuation = yes ; #初试构象不约束,不复位,用于精确的继续计算或重计算
constraint_algorithm = lincs ; #约束算法 lincs :不能用于角度约束
constraints = all-bonds ; #键约束,all-bonds:所有键约束
lincs_iter = 1 ; #迭代次数,用于LINCS约束精度,默认1
lincs_order = 4 ; #约束偶合矩阵阶次,用于LINCS约束精度,默认4
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; #邻近列表搜索方法
nstlist = 10 ; #邻近列表更新频率
rcoulomb = 1.4 ; #短程库伦截断
rvdw = 1.4 ; #短程范德华力截断
; Electrostatics
coulombtype = PME ; #库伦计算方式
pme_order = 4 ; #PME插值,默认4表示3次插值
fourierspacing = 0.16 ; #FFT傅里叶变换格点间距,默认。。。,与PME同时使用
; Temperature coupling
tcoupl = V-rescale ; #指定热耦合方法
tc-grps = Protein_JZ4 Water_and_ions ; #热偶合组
tau_t = 0.1 0.1 ; #热偶合时间常数
ref_t = 300 300 ; #参考温度--恒温值,个数对应组
; Pressure coupling
pcoupl = Parrinello-Rahman ; #指定压力耦合方式 ;Parrinello-Rahman:
pcoupltype = isotropic ; #isotropic:盒子各向同性
tau_p = 2.0 ; #压力耦合时间常数
ref_p = 1.0 ; #参考压力---恒压值,一般为1 bar
compressibility = 4.5e-5 ; #水可压缩性,1 bar300K时为4.5e-5 bar-1
; Periodic boundary conditions
pbc = xyz ; #周期性边界条件;xyz:使用周期性边界条件
; Dispersion correction
DispCorr = EnerPres ; #色散校正
; Velocity generation
gen_vel = no ; #速度生成;no:不生成速度。输入文件没有速度,则为0;
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