制作仿真盒子

 gmx solvate -box 2.5 2.5 5 -cs spc216.gro -o water_39_test.gro 

再做top

讯享网vi water_39_test.top 

#include "oplsaa.ff/forcefield.itp" #include "oplsaa.ff/spce.itp" #include "oplsaa.ff/ions.itp" [ system ] ; Name water [ molecules ] ; Compound #mols SOL 1040 

做模拟

能量最小化

讯享网gmx grompp -f minim.mdp -c water_39_test.gro -p water_39_test.top -o water_39_minim.tpr gmx mdrun -v -deffnm water_39_minim 

nvt

gmx grompp -f nvt_38.mdp -c water_39_minim.gro -p water_39_test.top -o water_39_nvt.tpr gmx mdrun -v -deffnm water_39_nvt 

npt

讯享网gmx grompp -f npt_38.mdp -c water_39_nvt.gro -p water_39_test.top -o water_39_npt.tpr gmx mdrun -v -deffnm water_39_npt 

计算介电常数

gmx dipoles -corr total -c water_39_npt.xvg -f water_39_npt.trr -s water_39_npt.tpr 

讯享网
这里得出结论：截止半径越大越接近理论值，模拟时间越长越接近理论值
可以不做nvt，这里为了后续工作做了nvt

主要mdp

minim.mdp

讯享网; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ;define = -DPOSRES ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform 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 nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 0.8 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 0.8 ; long range electrostatic cut-off rvdw = 0.8 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions 

nvt_38.mdp

title = Protein-ligand complex NVT equilibration ;define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md ; leap-frog integrator nsteps =  ; 1 * 100 = 100 ps dt = 0.001 ; 1 fs ; Output control nstxout = 1000 ; save coordinates every 1.0 ps nstvout = 1000 ; save velocities every 1.0 ps nstenergy = 1000 ; save energies every 1.0 ps nstlog = 1000 ; update log file every 1.0 ps energygrps = system ; 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 ; short-range electrostatic cutoff (in nm) rvdw = 1 ; 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 = system ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 298 ; 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 = 298 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed 

npt_38.mdp

讯享网title = Protein-ligand complex NPT equilibration ;define = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand ; Run parameters integrator = md ; leap-frog integrator nsteps =  ; 1.9ns dt = 0.001 ; 1 fs ; Output control nstxout = 1000 ; save coordinates every 1.0 ps nstvout = 1000 ; save velocities every 1.0 ps nstenergy = 1000 ; save energies every 1.0 ps nstlog = 1000 ; update log file every 1.0 ps energygrps = ; 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 = 1.5 ; short-range electrostatic cutoff (in nm) rvdw = 1.5 ; 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 = system ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 298 ; 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