martini-能量最小化参数（mdp文件）

Posted 2020-10-15 谢小顿

  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