||
(十二)体系平衡
1.设定对配体的限制:
$gmx/genrestr -f jz4.gro -o posre_jz4.itp -fc 1000 1000 1000
** -f jz4.gro 输入配体的gro文件
** -o posre_jz4.itp 输出加了限制的配体itp文件
** -fc 1000 1000 1000 限制Force constants (kJ/mol nm^2)
2. 将限制的配体itp文件加入到topol.top中并保存:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include ligand topology
#include "drg.itp"
; Ligand position restraints
#ifdef POSRES
#include "posre_jz4.itp"
#endif
; Include water topology
#include "gromos43a1.ff/spc.itp"
3.
$gmx/make_ndx -f em.gro -o index.ndx
系统显示:
0 System : 33037 atoms
1 Protein : 1693 atoms
2 Protein-H : 1301 atoms
3 C-alpha : 163 atoms
4 Backbone : 489 atoms
5 MainChain : 653 atoms
6 MainChain+Cb : 805 atoms
7 MainChain+H : 815 atoms
8 SideChain : 878 atoms
9 SideChain-H : 648 atoms
10 Prot-Masses : 1693 atoms
11 non-Protein : 31344 atoms
12 Other : 15 atoms
13 JZ4 : 15 atoms
14 CL : 6 atoms
15 Water : 31323 atoms
16 SOL : 31323 atoms
17 non-Water : 1714 atoms
18 Ion : 6 atoms
19 JZ4 : 15 atoms
20 CL : 6 atoms
21 Water_and_ions : 31329 atoms
此时我们将蛋白(1 Protein)与配体(13 JZ4)融合:
> 1 | 13
> q #退出make_ndx
4. 设定NVT系综下体系平衡的配置文件nvt.mdp
用记事本编辑如下参数,保存为nvt.mdp:
title = Protein-ligand complex NVT 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 = no ; 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 = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
5.grompp预处理——NVT系综的体系平衡
$gmx/grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
6. NVT系综运行体系平衡
$gmx/mdrun -deffnm nvt
7. 设定NPT系综下体系平衡的配置文件npt.mdp
用记事本编辑如下参数,保存为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
8.grompp预处理——NPT系综的体系平衡
$gmx/grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
9.NPT系综运行体系平衡
$gmx/mdrun -deffnm npt
至此,体系平衡已经大功告成,(温度,压力均已确定)
(十三)动力学模拟
$gmx/grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_1.tpr
$gmx/mdrun -deffnm md_0_1
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