mdp文件-Chapter4-MD.mdp

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！