转载请注明出处！！！
本篇是对这篇文章的改进，解决了xy方向的周期问题，具体原理请见上面的文章，本篇只简述过程。仿真过程用的是alpha-tubulin和beta-tubulin

制作蛋白夹水层

这里制作的收敛水层，要在z轴的负方向上给个余量，这样就可以成功进行nwall =2的模拟了。

gmx editconf -f small_water_npt.gro -c -box 5.112 4.920 5 -o small_water_npt_center.gro

然后还是用packmol做整体的结构

vi center_224.inp
packmol < center_224.inp

center_224.inp

tolerance 1.0
filetype pdb
output center_224.pdbstructure chain_A.pdbnumber 1inside box 0. 0. 0. 60. 60. 60.constrain_rotation x 0. 20.constrain_rotation y 0. 20.
end structurestructure small_water_npt_center.pdbnumber 1inside box 0. 0. 60. 60. 60. 85.
end structurestructure chain_B.pdbnumber 1inside box 0. 0. 85. 60. 60. 145.constrain_rotation x 0. 20.constrain_rotation y 0. 20.
end structure

然后要做成gro

gmx editconf -f small_water_npt_center.pdb -o small_water_npt_center.gro

根据packmol中的大小改gro的尺寸

  6.00000   6.00000   14.50000

再做个top

vi center_224.top

这是根据small_water.topz中有1487个sol得来的
center_224.top

#include "oplsaa.ff/forcefield.itp"
;#include "metal.itp"
;#include "mPlus.itp"
;#include "mMinus.itp"
#include "two_test_Protein_chain_A.itp"
#include "two_test_Protein_chain_B.itp"#include "oplsaa.ff/spc.itp"
#include "oplsaa.ff/ions.itp"#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz1    1       1000       1000       1000
#endif[ system ]
; Name
Water In Sheets and protein[ molecules ]
; Compound       #molsProtein_chain_A  1SOL         1456
NA               31
Protein_chain_B  1

这里直接放离子平衡后的top了

gromacs仿真

离子平衡

gmx grompp -f ions.mdp -c center_224.gro -p center_224.top -o center_224_ions.tpr
gmx genion -s center_224_ions.tpr -o center_224_ions_finish.gro -p center_224.top -pname NA -np 31

能量最小化

gmx grompp -f em1.mdp -c center_224_ions_finish.gro -p center_224.top -o center_224_em.tpr
gmx mdrun -v -deffnm center_224_em

能量最小化之后的图

制作索引

索引在能量最小化制作，也就是nvt的前一步，这样最准确

gmx make_ndx -f center_224_em.gro -o center_224_em.ndx

最后nvt

gmx grompp -f nvt_second.mdp -c center_224_em.gro -p center_224.top -o center_224_nvt_xy.tpr
gmx mdrun -v -deffnm center_224_nvt_xy

两蛋白结合了

介电常数相关

gmx dipoles -corr total -c center_224_nvt_xy.xvg -f center_224_nvt_xy.trr -s center_224_nvt_xy.tpr
gmx dielectric -f center_224_nvt_xy.xvg -eps0 11.6619 -ffn aexp -o center_224_nvt_xy_freq.xvg -nsmooth 10

静止介电常数 11.6619
频响

相关mdp

ions.mdp

ions.mdp - used as input into grompp to generate ions.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     = cutoff    ; Treatment of long range electrostatic interactions rcoulomb        = 1       ; Short-range electrostatic cut-off rvdw            = 1       ; Short-range Van der Waals cut-off pbc             = xyz       ; Periodic Boundary Conditions in all 3 dimensions

em1.mdp

; Run Control
integrator  = steep        ; A steepest descent algorithm for energy minimization
emtol       = 100      ; Stop minimization when the maximum force < 100.0 kJ/mol/nm
emstep      = 0.01     ; [nm] initial step-size
nsteps      = 50000        ; Maximum number of (minimization) steps to perform; Output Control
nstlog      = 1        ; # of steps that else between writing energies to the log file
nstenergy   = 1        ; # of steps that else between writing energies to energy file; Neighbor searching and nonbonded interaction
cutoff-scheme   = verlet   ; Cutoff-related parameters
nstlist     = 1        ; Frequency to update the neighbor list and the long-range forces
ns_type     = grid     ; Method to determine neighbor list (simple, grid)
pbc     = xyz      ; Use periodic boundary conditions in all directions
rlist       = 0.5      ; [nm] Cut-off for making neighbor list (short range forces; Electrostatics
coulombtype = PME      ; Treatment of long range electrostatic interactions
rcoulomb    = 0.5      ; [nm] Short-range electrostatic cut-off; Van der waals
vdwtype     = cutoff
rvdw        = 0.5      ; [nm] Short-range Van der Waals cut-off; Temperature and pressure coupling are off during EM
tcoupl          = no       ; No temperature coupling
pcoupl          = no       ; No pressure coupling (fixed box size); No velocities during EM
gen_vel          = no      ; Do not generate velocities; options for bonds
constraints      = h-bonds     ; No contraints except those defined in the topology

nvt_second.mdp

; Run Control
integrator  = md       ; leap-frog integrator of Newton's equations of motion
tinit       = 0        ; [ps] starting time for the run
dt      = 0.002        ; 2 fs - [ps] time step for integration
nsteps      = 50000    ; 0.1 ns; Output Control
nstxout     = 1000     ; save coordinates every 2 ps
nstenergy   = 500      ; save energies every 1 ps
nstlog      = 50000        ; update log file every 100 ps; Bond parameters
continuation    = no       ; apply constraints to the start configuration and reset shells
constraints     = h-bonds  ; convert all bonds to constraints
constraint-algorithm = lincs   ; holonomic constraints ; Neighbor searching and nonbonded interactions
cutoff-scheme   = verlet   ; Cutoff-related parameters
nstlist     = 20       ; Frequency to update the neighbor list and the long-range forces
ns_type     = grid     ; Method to determine neighbor list (simple, grid)
pbc     = xy       ; Use periodic boundary conditions in all directions
rlist       = 1.2      ; [nm] Cut-off for making neighbor list (short range forces)
ewald-geometry  = 3dc
nwall           = 2
wall-atomtype   = MW MW
wall-type       = 12-6; Electrostatics
coulombtype = PME      ; Treatment of long range electrostatic interactions
rcoulomb    = 1.2      ; [nm] Short-range electrostatic cut-off; Van der waals
vdwtype     = cutoff
rvdw        = 1.2      ; [nm] Short-range Van der Waals cut-off;                    Do I need pme-order and fourier spacing?;pme_order = 4        ; cubic interpolation
;fourierspacing = 0.16     ; grid spacing for FFT; Temperature coupling
tcoupl      = v-rescale    ; Temperature coupling, modified Berendsen thermostat‬
tc_grps         = system   ; Group to couple to separate temperature baths
tau_t           = 0.1      ; [ps] Time constant for coupling
ref_t           = 300      ; [K] Reference temperature for coupling; Pressure coupling is off for NVT
Pcoupl          = No       ; No pressure coupling (fixed box size); Generate velocities to start
gen_vel     = yes      ; assign velocities from Maxwell distribution
gen_temp    = 300      ; temperature for Maxwell distribution
gen_seed    = -1       ; generate a random seed; Freeze Sheets
;freezegrps      = backbone
;freezedim       = Y Y Y

创作不易，转载请注明出处！！！谢谢！

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制作仅在xy方向有周期性的夹层结构，且不使用约束平板