• 输入参数：一个典型的mdp文件

  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 ; TIMESTEP IN MARTINI
  11 ; Most simulations are numerically stable
  12 ; with dt=40 fs, some (especially rings and polarizable water) require 20-30 fs.
  13 ; Note that time steps of 40 fs and larger may create local heating or
  14 ; cooling in your system. Although the use of a heat bath will globally
  15 ; remove this effect, it is advised to check consistency of
  16 ; your results for somewhat smaller time steps in the range 20-30 fs.
  17 ; Time steps exceeding 40 fs should not be used; time steps smaller
  18 ; than 20 fs are also not required unless specifically stated in the itp file.
  19 ; 时间步长：不要大于40，不要小于20.20-30fs是一个很好的选择。
  20
  21 integrator = md
  22 dt = 0.04
  23 nsteps = 50000
  24 nstcomm = 10 ;质心移动的频率
  25 comm-grps = ;对质心的分组，默认为整个系统
  26
  27 nstxout = 0
  28 nstvout = 0
  29 nstfout = 0
  30 nstlog = 1000
  31 nstenergy = 100
  32 nstxtcout = 1000 ;number of steps that elapse between writing position coordinates using lossy compression 每隔几步输出一次低精度坐标值
  33 xtc_precision = 100 ;轨迹压缩文件的精度
  34 xtc-grps = ;轨迹压缩文件内部的分组
  35 energygrps = DPPC W
  36
  37 ; NEIGHBOURLIST and MARTINI
  38 ; Due to the use of shifted potentials, the noise generated
  39 ; from particles leaving/entering the neighbour list is not so large,
  40 ; even when large time steps are being used. In practice, once every
  41 ; ten steps works fine with a neighborlist cutoff that is equal to the
  42 ; non-bonded cutoff (1.2 nm). However, to improve energy conservation
  43 ; or to avoid local heating/cooling, you may increase the update frequency
  44 ; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option
  45 ; is computationally less expensive and leads to improved energy conservation
  46 ;由于使用了漂移势，临近列表的噪声较大。一般将刷新频率设为10，截断距离设为1.2nm，不过为了更好地精度，截断距离也可设为1.4nm，这样既可以获得更高精度，
  47 ;也不会带来过多的计算量。
  48
  49 nstlist = 10
  50 ns_type = grid
  51 pbc = xyz
  52 rlist = 1.4 ; 截断距离，1.4nm以外的不再视为键合和近邻作用
  53
  54 ; MARTINI and NONBONDED
  55 ; Standard cut-off schemes are used for the non-bonded interactions
  56 ; in the Martini model: LJ interactions are shifted to zero in the
  57 ; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2 nm.
  58 ; The treatment of the non-bonded cut-offs is considered to be part of
  59 ; the force field parameterization, so we recommend not to touch these
  60 ; values as they will alter the overall balance of the force field.
  61 ; In principle you can include long range electrostatics through the use
  62 ; of PME, which could be more realistic in certain applications
  63 ; Please realize that electrostatic interactions in the Martini model are
  64 ; not considered to be very accurate to begin with, especially as the
  65 ; screening in the system is set to be uniform across the system with
  66 ; a screening constant of 15. When using PME, please make sure your
  67 ; system properties are still reasonable.
  68 ; 标准截断被用于Martini模型中的非键合作用：LJ作用在0.9-1.2nm之间变为0，并且静电作用发生在0-1.2nm之内。
  69 ; 对非键合力的处理是经过仔细考虑了买我们建议你不要乱动。原则上，你可以将长程静电力也纳入考虑，通过使用PME方法，这在一些情况下会更精确。
  70 ; 请注意，在Martini模型中，静电作用从一开始就是不精确的，当使用PME时，请确认你的系统性质仍然是合理的
  71 ; With the polarizable water model, the relative electrostatic screening
  72 ; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
  73 ; apolar solvent. The polarizable water itself will perform the explicit screening
  74 ; in aqueous environment. In this case, the use of PME is more realistic.
  75 ; 在可极化水模型中，相关的静电筛选（epsilon-r）应该取2.5，代表一个低的无极化溶液。
  76 ; For use in combination with the Verlet-pairlist algorithm implemented
  77 ; in Gromacs 4.6 a straight cutoff in combination with the potential
  78 ; modifiers can be used. Although this will change the potential shape,
  79 ; preliminary results indicate that forcefield properties do not change a lot
  80 ; when the LJ cutoff is reduced to 1.1 nm. Be sure to test the effects for
  81 ; your particular system. The advantage is a gain of speed of 50-100%.
  82 ;
  83
  84 coulombtype = Shift ; 在某个位置将势能设为常数（0）
  85 ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
  86 rcoulomb_switch = 0.0 ;where to start switching the Coulomb potential, only relevant when force or potential switching is used
  87 ; 在何处开启库仑势
  88 rcoulomb = 1.2
  89 ;distance for the Coulomb cut-off 截断距离
  90 epsilon_r = 15 ;The relative dielectric constant. A value of 0 means infinity.
  91 ; 2.5 (with polarizable water)
  92 vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
  93 rvdw_switch = 0.9
  94 rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
  95
  96 ;cutoff-scheme = verlet
  97 ;coulomb-modifier = Potential-shift
  98 ;vdw-modifier = Potential-shift
  99 ;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity,即截断距离之外的静电常数为无穷大
  100 ;verlet-buffer-drift = 0.005
  101
  102 ; MARTINI and TEMPERATURE/PRESSURE
  103 ; normal temperature and pressure coupling schemes can be used. 正常的温度和压力耦合就可以
  104 ; It is recommended to couple individual groups in your system separately. 建议分组耦合
  105 ; Good temperature control can be achieved with the velocity rescale (V-rescale) 使用速度重整化恒温器，耦合时间常数设为1ps。
  106 ; thermostat using a coupling constant of the order of 1 ps. Even better 当然使用0.1ps效果就更好了，但这样的耦合就不能称之为弱耦合了
  107 ; temperature control can be achieved by reducing the temperature coupling
  108 ; constant to 0.1 ps, although with such tight coupling (approaching
  109 ; the time step) one can no longer speak of a weak-coupling scheme.
  110 ; We therefore recommend a coupling time constant of at least 0.5 ps. 我们推荐耦合时间常数最少为0.5ps
  111 ; The Berendsen thermostat is less suited since it does not give Berendsen恒温器不太适用，因为他不能给出一个良好的系综
  112 ; a well described thermodynamic ensemble.
  113 ;
  114 ; Pressure can be controlled with the Parrinello-Rahman barostat, 压力可用P-R恒压。耦合时间常数在4-8ps之间。
  115 ; with a coupling constant in the range 4-8 ps and typical compressibility 注意到，为了平衡，Berendsen恒温器可能产生更好的效果，因为P-R易于被扰动。
  116 ; in the order of 10-4 - 10-5 bar-1. Note that, for equilibration purposes,
  117 ; the Berendsen thermostat probably gives better results, as the Parrinello-
  118 ; Rahman is prone to oscillating behaviour. For bilayer systems the pressure 对于双层膜系统，压力耦合应该是半各向异性。
  119 ; coupling should be done semiisotropic.
  120
  121 tcoupl = v-rescale
  122 tc-grps = DPPC W
  123 tau_t = 1.0 1.0
  124 ref_t = 320 320
  125 Pcoupl = parrinello-rahman
  126 Pcoupltype = semiisotropic
  127 tau_p = 12.0 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
  128 compressibility = 3e-4 3e-4
  129 ref_p = 1.0 1.0
  130
  131 gen_vel = no
  132 gen_temp = 320
  133 gen_seed = 473529
  134
  135 ; MARTINI and CONSTRAINTS
  136 ; for ring systems and stiff bonds constraints are defined
  137 ; which are best handled using Lincs.
  138
  139 constraints = none
  140 constraint_algorithm = Lincs
  141 unconstrained_start = no; 启动时不做限制：no（对初始构象做限制，重构壳层），yes（不对初始构象做限制）
  142 lincs_order = 4
  143 lincs_warnangle = 30

时间步长：推荐将时间步长设为20-30 fs, 同时使用更大的邻区列表截断(到1.4 nm).

温度与压力耦合时间常数：好的温度控制可以使用Berendsen方法, 耦合常数的数量级为τ= 1 ps.压力可采用Berendsen方法进行控制, 耦合常数的范围在1-5 ps之间, 典型的压缩系数为10-4-10-3 bar-1. 需要注意的是, 为了估算CG模拟的压缩系数, 你应该使用Parrinello-Rahman耦合方法.

配对列表(pairlist)以及配对列表截断(pairlist cutoff)：10步一次，1.4或1.2nm

截断(cutoffs)的选择：对于非键作用, 使用标准的截断(cutoff)方案: LJ相互作用在0.9-1.2 nm的范围内被调整为0, 静电相互作用的调整范围为0.0-1.2 nm. 对非键截断的处理是力场参数化的一部分, 最好不要去碰这些值, 因为这可能会改变力场的整体平衡.

PME与反应力场：原则上是可以用的, 尽管Martini力场参数化时使用短程移位静电相互作用. 使用反应力场(也可等效为移位势能)可能不会对模拟有太大影响. 另一方面, PME可能导致模拟行为显著不同, 在某些应用中可能更真实(如在枝状聚合物和抑菌多肽攻击脂质双层膜的模拟中可以看到真实的膜孔). 需要注意的是, Matini模型中的静电相互作用并不是很精确, 尤其整个系统的屏蔽被设为均匀的, 具有相同的屏蔽常数15. 当使用PME时, 请确保体系的性质仍然是合理的.PME可以与极化Martini水模型结合使用, 并且是合理的, 因为静电相互作用更真实.