GROMACS运行参数之npt.mdp文件详解

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npt平衡过程中需要用到输入文件npt.mdp，现对里面的各种编辑项目做简单注释。

###npt.mdp###

title       = Protein-ligand complex NPT 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    = 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
refcoord_scaling    = com
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no        ; velocity generation off after NVT 

中文注释仅供参考

###npt.mdp###

title       = Protein-ligand complex NPT 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    = 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
refcoord_scaling    = com    #  
; 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；