终于到了mdp系列的第四篇，最终MD模拟的mdp文件
先上代码，md.mdp
1 title = OPLS Lysozyme MD simulation 2 ; Run parameters 3 integrator = md ; leap-frog integrator 4 nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns) 5 dt = 0.002 ; 2 fs 6 ; Output control 7 nstxout = 5000 ; save coordinates every 10.0 ps 8 nstvout = 5000 ; save velocities every 10.0 ps 9 nstenergy = 5000 ; save energies every 10.0 ps 10 nstlog = 5000 ; update log file every 10.0 ps 11 nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps 12 ; nstxout-compressed replaces nstxtcout 13 compressed-x-grps = System ; replaces xtc-grps 14 ; Bond parameters 15 continuation = yes ; Restarting after NPT 16 constraint_algorithm = lincs ; holonomic constraints 17 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained 18 lincs_iter = 1 ; accuracy of LINCS 19 lincs_order = 4 ; also related to accuracy 20 ; Neighborsearching 21 cutoff-scheme = Verlet 22 ns_type = grid ; search neighboring grid cells 23 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme 24 rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) 25 rvdw = 1.0 ; short-range van der Waals cutoff (in nm) 26 ; Electrostatics 27 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 28 pme_order = 4 ; cubic interpolation 29 fourierspacing = 0.16 ; grid spacing for FFT 30 ; Temperature coupling is on 31 tcoupl = V-rescale ; modified Berendsen thermostat 32 tc-grps = Protein Non-Protein ; two coupling groups - more accurate 33 tau_t = 0.1 0.1 ; time constant, in ps 34 ref_t = 300 300 ; reference temperature, one for each group, in K 35 ; Pressure coupling is on 36 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT 37 pcoupltype = isotropic ; uniform scaling of box vectors 38 tau_p = 2.0 ; time constant, in ps 39 ref_p = 1.0 ; reference pressure, in bar 40 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 41 ; Periodic boundary conditions 42 pbc = xyz ; 3-D PBC 43 ; Dispersion correction 44 DispCorr = EnerPres ; account for cut-off vdW scheme 45 ; Velocity generation 46 gen_vel = no ; Velocity generation is off
注意，这里已经不再采用位置限定性模拟了，因此也就没有了define = -DPOSRES 这一行。
NVT模拟中不采用压力耦合，NPT模拟中不采用温度耦合，MD模拟中二者都要用上，这才是最接近于真实的情况，即温度要与外界一致，压力也要与外界一致。需要说明的部分均在minim.mdp、nvt.mdp、npt.mdp中说明过了，这里不再赘述。
mdp系列到此告一段落，有机会再写Chapter5吧！