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 defined102 ; which are best handled using Lincs. 103 104 constraints              = none 105 constraint_algorithm     = Lincs106 continuation             = no107 lincs_order              = 4108 lincs_warnangle          = 30