【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
个人公众号,比较懒,很少更新,可以在上面提问题,如果回复不及时,可发邮件给我: tiehan@sina.cn

Sam avatar
About Sam
专注生物信息 专注转化医学