分子动力学模拟学习2-Gromacs运行分子动力学模拟
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1. 把上一步生成的Enzyme.gro和Enzyme.top文件改个名字
cp Enzyme.top topol.top
cp Enzyme.gro complex.gro
2. 能量最小化
首先准备能量最小化mdp文件 em_real.mdp ，示例如下
; minim.mdp - used as input into grompp to generate real_em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
gmx grompp -f em_real.mdp -c complex.gro -r complex.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em
AI写代码
em_real.mdp文件中的各项参数说明：
（1）integrator:
=steep:用最陡下降法做能量极小化。
=cg:用共现桃度法做能量极小化(不支持约束)。
=l-bigs:用L-BFGS法做能量极小化。
=nm:做正则振动分析( 必须双精度版)。
（2）emtol: 能量极小化时最大受力小于多少就认为收敛(kJ/mol/nm).默认为10.0。
当最大作用力小于此值，认为最小化过程收敛。一般蛋白-配体中是1000、500。
（3）emstep: 最陡下降法最大步长(nm)。默认0.01。
（4）nsteps: 动力学或能量极小化的步数上限,指定最大迭代次数。
之后运行能量最小化
gmx grompp -f em_real.mdp -c complex.gro -r complex.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em
3. NVT平衡
首先准备NVT所需mdp文件 nvt.mdp ，示例如下：
title = NVT
define = -DPOSRES ; position restrain the protein
; 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
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = shake ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
shake-SOR = no
shake-tol = 0.0001
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; 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 is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
AI写代码
关于各参数的含义，参见后面md.mdp文件中的参数解释。
需要注意的是，前面我们利用的AmberTools来产生top文件，因此如果我们这里用POSRES来做位置约束的话，需要将topol.top文件中的ifdef flexible修改为ifdef POSRES，否则此步中会出现warning。
之后运行NVT平衡
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
gmx mdrun -deffnm nvt
4. NPT平衡
同样，首先准备NPT所需的 npt.mdp 文件
title = NPT
define = -DPOSRES ; position restrain the protein
; 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
; Bond parameters
continuation = yes ; Restarting after NVT
constraint_algorithm = shake ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
shake-SOR = no
shake-tol = 0.0001
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; 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 is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in 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
; Velocity generation
gen_vel = no ; Velocity generation is off
AI写代码
之后运行NPT
gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
gmx mdrun -deffnm npt
5. 成品模拟
md.mdp 文件示例如下
title = MD
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000000 ; 2 * 50000000 = 100000 ps (100 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress bulky .trr file by specifying
nstvout = 0 ; 0 for output frequency of nstxout,
nstfout = 0 ; nstvout, and nstfout
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = shake ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
shake-SOR = no
shake-tol = 0.0001
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; 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 is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; 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 is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in 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
; 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 is off
AI写代码
md.mdp文件中各项参数含义：
（1）title=MD：标题，可任意定义（最长64个字）
（2）define：常涉及到的是-DFLEXIBLE，会使水分子不被SETTLES算法约束成刚性。当利用posre.itp对位置进行限制时可用-DPOSRES使之生效.
（3）integrator: 决定当前任务干什么。
=md (默认) ：leap-frog( md蛙跳算法)方式做动力学。
=md-vv：用Velocity-Verlet方式做动力学，在功能上有一些限制。
=sd：做随机动力学(Langevin动力学)。
=bd：做布朗动力学。
（4） tinit：动力学开始的时间(ps)。 默认0
（5） dt：动力学步长(ps)。默认0.001 (1fs)，一般我们都使用0.002。
（6）nsteps：动力学或能量极小化的步数上限,指定最大迭代次数。
（7）init-step： 起始步数, 对非平衡模拟, 精确重启或重做某部分模拟时, 设定为重启步编号。
（8）nstxout = 0：输出trr坐标10000
nstvout = 0：输出trr速度 10000
nstfout = 0：输出trr受力 10000
nstxtcout = 5000：如果这个数比前三者小的多，那么其就会很大，比trr都大。
compressed-x-precision =5000：写入xtc轨迹的精确度。默认为 (1000)
compressed-x-grps：选择输出到xtc文件里的group， 默认为system。该参数只影响xtc轨迹，不影响trr轨迹。如果想在做动力学的时候就只把蛋白写入轨迹文件中，可以mdp中设compressed-x-grps = non-water。一般我们用体系即可。之后再根据需要用trjconv来处理获得包含水的轨迹文件。
nstlog=5000：每多少步输出一次各种能量信息到log文件，默认为1000。
nstenergy:每多少步输出一次能量信息到.edr文件，默认为1000。
（9）constraini-algorithm ；设定约束算法
=LINCS（默认）:使用LINCS方法约束，但不能约束键角。
=SHAKE：使用SHAKE方法约束，没LINCS可靠不能用于能量极小化。
之后运行md.mdp
gmx grompp -f md.mdp -c npt.gro -r npt.gro -t npt.cpt -p topol.top -o md.tpr
gmx mdrun -deffnm md
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