1 ;
2 ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
3 ; Updated 02 feb 2013 by DdJ
4 ;
5 ; for use with GROMACS 4.5/4.6
6 ;
7
8 title = Martini
9
10
11 ; TIMESTEP IN MARTINI
12 ; Most simulations are numerically stable
13 ; with dt=40 fs, some (especially rings and polarizable water) require 20-30 fs.
14 ; Note that time steps of 40 fs and larger may create local heating or
15 ; cooling in your system. Although the use of a heat bath will globally
16 ; remove this effect, it is advised to check consistency of
17 ; your results for somewhat smaller time steps in the range 20-30 fs.
18 ; Time steps exceeding 40 fs should not be used; time steps smaller
19 ; than 20 fs are also not required unless specifically stated in the itp file.
20 ; 时间步长最好不超过40fs 例如本文件中用的就是40fs 0.04ps=40fs
21
22 integrator = steep ; Run steepest descent energy minimization algorithm
23 dt = 0.04
24 nsteps = 50000 ; Number of steep steps to run
25 nstcomm = 100
26 comm-grps =
27
28
29 ; OUTPUT CONTROL OPTIONS =
30 ; Output frequency for coords (x), velocities (v) and forces (f) =
31
32 nstxout = 5000
33 nstvout = 5000
34 nstfout = 0
35 nstlog = 1000 ; Output frequency for energies to log file
36 nstenergy = 100 ; Output frequency for energies to energy file
37 nstxout-compressed = 1000 ; Output frequency for .xtc file 向xtc文件中输出的频率
38 compressed-x-precision = 100
39 xtc-grps =
40 energygrps = System
41
42
43 ; NEIGHBOURLIST and MARTINI
44 ; Due to the use of shifted potentials, the noise generated 由于使用了漂移势，粒子进入/离开近邻列表带来的影响不是特别大
45 ; from particles leaving/entering the neighbour list is not so large, 即使时间步长很长的时候
46 ; even when large time steps are being used. In practice, once every 在实践中，每十步更新一次就很不错，近邻列表的截断距离与非键合力的
47 ; ten steps works fine with a neighborlist cutoff that is equal to the 截断距离取为相等，1.2nm
48 ; non-bonded cutoff (1.2 nm). However, to improve energy conservation 但是 为了提高能量的稳定性，避免局部的加热、冷却，有时候会增加更新频率
49 ; or to avoid local heating/cooling, you may increase the update frequency 或者扩大截断距离到1.4nm
50 ; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option 扩大到1.4nm是一个很好的选择，既可以较少计算又可以提高能量稳定性
51 ; is computationally less expensive and leads to improved energy conservation
52
53 nstlist = 10
54 ns_type = grid
55 pbc = xyz
56 rlist = 1.2
57
58 ; MARTINI and NONBONDED
59 ; Standard cut-off schemes are used for the non-bonded interactions
60 ; in the Martini model: LJ interactions are shifted to zero in the
61 ; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2 nm.
62 ; The treatment of the non-bonded cut-offs is considered to be part of
63 ; the force field parameterization, so we recommend not to touch these
64 ; values as they will alter the overall balance of the force field.
65 ; In principle you can include long range electrostatics through the use
66 ; of PME, which could be more realistic in certain applications
67 ; Please realize that electrostatic interactions in the Martini model are
68 ; not considered to be very accurate to begin with, especially as the
69 ; screening in the system is set to be uniform across the system with
70 ; a screening constant of 15. When using PME, please make sure your
71 ; system properties are still reasonable.
72 ;
73 ; With the polarizable water model, the relative electrostatic screening
74 ; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
75 ; apolar solvent. The polarizable water itself will perform the explicit screening
76 ; in aqueous environment. In this case, the use of PME is more realistic.
77 ;
78 ; For use in combination with the Verlet-pairlist algorithm implemented
79 ; in Gromacs 4.6 a straight cutoff in combination with the potential
80 ; modifiers can be used. Although this will change the potential shape,
81 ; preliminary results indicate that forcefield properties do not change a lot
82 ; when the LJ cutoff is reduced to 1.1 nm. Be sure to test the effects for
83 ; your particular system. The advantage is a gain of speed of 50-100%.
84
85 coulombtype = cut-off ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
86 rcoulomb_switch = 0.0
87 rcoulomb = 1.2
88 epsilon_r = 15 ; 2.5 (with polarizable water)
89 vdw_type = cut-off ;cutoff (for use with Verlet-pairlist)
90 rvdw_switch = 0.9
91 rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
92
93 ;cutoff-scheme = verlet
94 ;coulomb-modifier = Potential-shift-Verlet
95 ;vdw-modifier = Potential-shift-Verlet
96 ;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
97 ;verlet-buffer-tolerance = 0.005
98
99
100 ; MARTINI and CONSTRAINTS
101 ; for ring systems and stiff bonds constraints are defined
102 ; which are best handled using Lincs.
103
104 constraints = none
105 constraint_algorithm = Lincs
106 continuation = no
107 lincs_order = 4
108 lincs_warnangle = 30