martini-参数（mdp）

  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