【3.3.7】gromacs参数文件
用于能量优化的参数文件 immin.mdp
Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment
title = Energy Minimization ; Title of run
cpp = /lib/cpp ; Preprocessor （预处理器）
define = -DFLEXIBLE （-DFLEXIBLE代表采用flexible SPC water模型，This allows steepest descents to minimize further.）
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol
nsteps = 500 ; Maximum number of (minimization) steps to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
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
ns_type = simple ; Method to determine neighbor list (simple, grid)(大的体系中grid速度快，网格搜索)
coulombtype = cut-off ; Treatment of long range electrostatic interactions（采用cut-off方式处理长程库伦作用力，还可选择Ewald、PME等方式）
rcoulomb = 1.0 ; long range electrostatic cut-off （长程库伦作用截断为1.0 nm）
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints （不限制键的伸缩运动）
pbc = no ; Periodic Boundary Conditions (yes/no) （能量优化时不采用周期性边界盒子）
约束蛋白，进行MD，放松溶剂 pr.mdp
; VARIOUS PREPROCESSING OPTIONS
title = Position Restrained Molecular Dynamics
cpp = /lib/cpp
define = -DPOSRES (进行约束，由posre.itp决定约束原子，在pdb2gmx时可产生)
; RUN CONTROL PARAMETERS
integrator = md （进行MD）
dt = 0.001 ; time step (ps) （步长为0.001 ps，1 fs）
nsteps = 2500 ; number of steps（进行2500步，2.5ps）
; OUTPUT CONTROL OPTIONS
nstenergy = 10 （每10步写一次能量数据）
energygrps = Protein Non-Protein （蛋白和非蛋白的能量分开写）
; NEIGHBORSEARCHING PARAMETERS
nstlist = 5（每隔5步更新一次周围原子信息，默认10）
ns_type = grid （搜索模式为grid）
pbc = xyz （在所用方向使用周期边界）
rlist = 0.9 （短程作用的cut-off）
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = Reaction-Field (采用的库伦作用方式)
rcoulomb = 1.4
epsilon_rf = 78 （相对介电常数，只在选择Reaction—Field时有）
vdw-type = Cut-off
rvdw = 1.4
; Temperature coupling
tcoupl = Berendsen （采用Berendsen方式偶和温度）
tc-grps = Protein Non-Protein （蛋白和非蛋白分开耦合）
tau_t = 0.1 0.1 （每组分别得耦合时间常数，0.1ps）
ref_t = 200 200 （热浴温度）
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes ; （采用Maxwell分布随机设置粒子速度）
gen_temp = 200.0 ; （以200K为标准设置温度）
gen_seed = 9999 ; （随机化种子，数不同，初始化速度状态不同）
; OPTIONS FOR BONDS
constraints = all-bonds ; （固定所有键长）
不约束蛋白，给体系升温至300K vnt.mdp
title = NVT simulation
cpp = /lib/cpp
integrator = md
dt = 0.002
nsteps = 1250
; OUTPUT CONTROL OPTIONS
nstxout = 0 （只输出最后一帧的坐标）
nstvout = 0 （只输出最后一帧速度）
nstfout = 0 （只输出最后一帧力）
nstlog = 1 ; Write every step to the log
nstenergy = 10 ; Write energies at every step
nstxtcout = 0 （不输出轨迹文件）
energygrps = Protein Non-Protein ;(分开为不同组写能量数据)
; NEIGHBORSEARCHING PARAMETERS
nstlist = 5
ns-type = Grid
pbc = xyz
rlist = 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = Reaction-Field
rcoulomb = 1.4
epsilon_rf = 78
vdw-type = Cut-off
rvdw = 1.4
; Temperature coupling
tcoupl = Berendsen
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
; Pressure coupling
pcoupl = no
; OPTIONS FOR BONDS
constraints = all-bonds
恒温，平衡压力 npt.mdp
title = NVT simulation cpp = /lib/cpp
integrator = md dt = 0.002
nsteps = 1250
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1
nstenergy = 10
nstxtcout = 0
xtc_precision = 1000 （轨迹写入精度？）
xtc-grps = System
energygrps = Protein Non-Protein
nstlist = 5
ns-type = Grid
pbc = xyz
rlist = 0.9
coulombtype = Reaction-Field
rcoulomb = 1.4
epsilon_rf = 78
vdw-type = Cut-off
rvdw = 1.4
Tcoupl = Berendsen
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
Pcoupl = Berendsen （耦合压力的方式）
Pcoupltype = Isotropic （各向同性耦合）
tau_p = 1.0 （耦合时间常数 1ps）
compressibility = 4.5e-5 （可压缩性，水在一个大气压时为此值）
ref_p = 1.0 （耦合参考气压，1个大气压）
gen_vel = yes ;
gen_temp = 300.0 ;
gen_seed = 9999 ;
constraints = all-bonds
Production MD
; VARIOUS PREPROCESSING OPTIONS
title = Production Simulation
cpp = /lib/cpp
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0 ; Starting time
dt = 0.002 ; 2 femtosecond time step for integration
nsteps = 5000000 ; Make it 10 ns
; OUTPUT CONTROL OPTIONS
nstxout = 50000 ; Writing full precision coordinates every nanosecond
nstvout = 50000 ; Writing velocities every nanosecond
nstfout = 0 ; Not writing forces
nstlog = 2500 ; Writing to the log file every step
nstenergy = 2500 ; Writing out energy information every step
nstxtcout = 2500 ; Writing coordinates every 5 ps（写xtc轨迹文件）
energygrps = Protein Non-Protein
; NEIGHBORSEARCHING PARAMETERS
nstlist = 5
ns-type = Grid
pbc = xyz
rlist = 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = Reaction-Field
rcoulomb = 1.4
epsilon_rf = 78
epsilon_r = 1
vdw-type = Cut-off
rvdw = 1.4
; Temperature coupling
Tcoupl = Berendsen
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
; Pressure coupling
Pcoupl = Berendsen
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
; OPTIONS FOR BONDS
constraints = all-bonds
constraint-algorithm = Lincs （采用Lincs算法固定亲，也可以是SHAKE）
unconstrained-start = yes （开始时不进行constraint）
lincs-order = 4 （下面是lincs的参数）
lincs-iter = 1
lincs-warnangle = 30
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