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nvt平衡过程中需要用到输入文件nvt.mdp,现对里面的各种编辑项目做简单注释。
###nvt.mdp###
title = Protein-ligand complex NVT equilibration
define = -DPOSRES ; position restrain the protein and ligand
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
energygrps = Protein JZ4
; Bond parameters
continuation = no ; 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 = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
中文注释仅供参考
###nvt.mdp###
title = Protein-ligand complex NVT equilibration #
define = -DPOSRES ; #预处理控制拓扑文件
; 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 = 50000 ; #积分或能量最小化步数
dt = 0.002 ; #积分步长
; Output control
nstxout = 500 ; #坐标保存到轨迹文件的频率
nstvout = 500 ; #速度保存到轨迹文件的频率
nstenergy = 500 ; #能量保存到轨迹文件的频率,必须是nstcalcenergy的倍数
nstlog = 500 ; # log文件更新频率
energygrps = Protein JZ4 #保存能量的组
; Bond parameters
continuation = no ; # no:初试构象约束,并复位,第一次MD
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 = no ; #指定压力耦合方式;no:不耦合,即固定盒子大小
; 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 = yes ; #速度生成 ;yes:根据麦克斯韦速度分布函数生成速度,只对md有意义
gen_temp = 300 ; #体系温度,用于麦克斯韦速度分布
gen_seed = -1 ; #初始速度初试随机数,-1表示为进程的ID数