分析梳理--分子动力学模拟的常规步骤三（Gromacs）

-f      [<.mdp>]           (grompp.mdp)
           grompp input file with MD parameters
 -c      [<.gro/.g96/...>]  (conf.gro)
           Structure file: gro g96 pdb brk ent esp tpr
 -r      [<.gro/.g96/...>]  (restraint.gro)  (Opt.)
           Structure file: gro g96 pdb brk ent esp tpr
 -rb     [<.gro/.g96/...>]  (restraint.gro)  (Opt.)
           Structure file: gro g96 pdb brk ent esp tpr
 -n      [<.ndx>]           (index.ndx)      (Opt.)
           Index file
 -p      [<.top>]           (topol.top)
           Topology file
 -t      [<.trr/.cpt/...>]  (traj.trr)       (Opt.)
           Full precision trajectory: trr cpt tng
 -e      [<.edr>]           (ener.edr)       (Opt.)
           Energy file
 -qmi    [<.inp>]           (topol-qmmm.inp) (Opt.)
           Input file for QM program

Options to specify input/output files:

 -ref    [<.trr/.cpt/...>]  (rotref.trr)     (Opt.)
           Full precision trajectory: trr cpt tng

Options to specify output files:

 -po     [<.mdp>]           (mdout.mdp)
           grompp input file with MD parameters
 -pp     [<.top>]           (processed.top)  (Opt.)
           Topology file
 -o      [<.tpr>]           (topol.tpr)
           Portable xdr run input file
 -imd    [<.gro>]           (imdgroup.gro)   (Opt.)
           Coordinate file in Gromos-87 format

Other options:

 -[no]v                     (no)
           Be loud and noisy
 -time   <real>             (-1)
           Take frame at or first after this time.
 -[no]rmvsbds               (yes)
           Remove constant bonded interactions with virtual sites
 -maxwarn <int>             (0)
           Number of allowed warnings during input processing. Not for normal
           use and may generate unstable systems
 -[no]zero                  (no)
           Set parameters for bonded interactions without defaults to zero
           instead of generating an error
 -[no]renum                 (yes)
           Renumber atomtypes and minimize number of atomtypes

; md.mdp - 分子动力学模拟参数文件

; 预处理器
cpp                 = /usr/bin/cpp
define              = -DPOSRES           ; 如需位置限制，取消注释

; 运行控制
integrator          = md                 ; 分子动力学积分器
tinit               = 0                  ; 起始时间 (ps)
dt                  = 0.002              ; 时间步长 (ps) = 2 fs
nsteps              = 5000000            ; 总步数 (5M * 2 fs = 10 ns)
comm-mode           = Linear
nstcomm             = 100                ; 质心运动移除频率

; 邻居搜索与短程相互作用
cutoff-scheme       = Verlet             ; 适用于GPU加速
nstlist             = 20                 ; 邻居列表更新频率
ns-type             = grid               ; 网格搜索算法
pbc                 = xyz                ; 周期性边界条件
rlist               = 1.0                ; 邻居列表截断距离 (nm)

; 静电相互作用
coulombtype         = PME                ; 粒子网格Ewald方法
rcoulomb            = 1.0                ; 静电截断距离 (nm)
pme-order           = 4                  ; PME插值阶数
fourierspacing      = 0.16               ; PME网格间距 (nm)

; 范德华相互作用
vdwtype             = Cut-off            ; 截断类型
rvdw                = 1.0                ; 范德华截断距离 (nm)
DispCorr            = EnerPres           ; 对能量/压力进行色散校正

; 温度耦合
tcoupl              = V-rescale          ; 速度重标定恒温器
tc-grps             = Protein Non-Protein; 温度耦合组
tau_t               = 0.1   0.1          ; 时间常数 (ps)
ref_t               = 298   298          ; 参考温度 (K)

; 压力耦合
pcoupl              = C-rescale          ; 恒压器（也可用 Parrinello-Rahman）
pcoupltype          = isotropic          ; 各向同性压力耦合
tau_p               = 2.0                ; 压力时间常数 (ps)
ref_p               = 1.0                ; 参考压力 (bar)
compressibility     = 4.5e-5             ; 压缩系数 (bar^-1)

; 约束算法
constraints         = h-bonds            ; 约束氢键（可用 all-bonds）
constraint-algorithm= LINCS              ; 约束算法
lincs-order         = 4                  ; LINCS阶数
lincs-iter          = 1                  ; LINCS迭代次数


; 输出频率
nstxout             = 0                  ; 不输出坐标文件 (旧格式)
nstvout             = 0                  ; 不输出速度
nstfout             = 0                  ; 不输出力
nstxout-compressed  = 1000               ; 每1000步输出压缩轨迹 (xtc)
nstenergy           = 1000               ; 每1000步输出能量文件 (edr)
nstlog              = 1000               ; 每1000步输出日志

; 其他选项
continuation        = no                 ; 从头开始模拟（非继续）
gen-vel             = yes                ; 生成初速度
gen-temp            = 298                ; 初速度对应温度
gen-seed            = -1                 ; 随机种子（-1 = 基于时间）

gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 3 -r solv.gro

Options to specify input files:

 -s      [<.tpr>]           (topol.tpr)
           Portable xdr run input file
 -n      [<.ndx>]           (index.ndx)      (Opt.)
           Index file

Options to specify input/output files:

 -p      [<.top>]           (topol.top)      (Opt.)
           Topology file

Options to specify output files:

 -o      [<.gro/.g96/...>]  (out.gro)
           Structure file: gro g96 pdb brk ent esp

Other options:

 -np     <int>              (0)
           Number of positive ions
 -pname  <string>           (NA)
           Name of the positive ion
 -pq     <int>              (1)
           Charge of the positive ion
 -nn     <int>              (0)
           Number of negative ions
 -nname  <string>           (CL)
           Name of the negative ion
 -nq     <int>              (-1)
           Charge of the negative ion
 -rmin   <real>             (0.6)
           Minimum distance between ions and non-solvent
 -seed   <int>              (0)
           Seed for random number generator (0 means generate)
 -conc   <real>             (0)
           Specify salt concentration (mol/liter). This will add sufficient
           ions to reach up to the specified concentration as computed from
           the volume of the cell in the input .tpr file. Overrides the -np
           and -nn options.
 -[no]neutral               (no)
           This option will add enough ions to neutralize the system. These
           ions are added on top of those specified with -np/-nn or -conc.

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 8

Select a continuous group of solvent molecules
Group     0 (         System) has 33892 elements
Group     1 (        Protein) has  1960 elements
Group     2 (      Protein-H) has  1001 elements
Group     3 (        C-alpha) has   129 elements
Group     4 (       Backbone) has   387 elements
Group     5 (      MainChain) has   517 elements
Group     6 (   MainChain+Cb) has   634 elements
Group     7 (    MainChain+H) has   646 elements
Group     8 (      SideChain) has  1314 elements
Group     9 (    SideChain-H) has   484 elements
Group    10 (    Prot-Masses) has  1960 elements
Group    11 (    non-Protein) has 31932 elements
Group    12 (          Water) has 31932 elements
Group    13 (            SOL) has 31932 elements
Group    14 (      non-Water) has  1960 elements
Select a group: 13
Selected 13: 'SOL'
Number of (3-atomic) solvent molecules: 10644