share/tutor/speptide/pr.mdp

   1 ;
   2 ;       User spoel (236)
   3 ;       Wed Nov  3 17:12:44 1993
   4 ;       Input file
   5 ;
   6 title               =  Yo
   7 cpp                 =  /lib/cpp
   8 define              =  -DPOSRES
   9 constraints         =  all-bonds
  10 integrator          =  md
  11 tinit               =  0.0
  12 dt                  =  0.002    ; ps !
  13 nsteps              =  5000     ; total 10 ps.
  14 nstcomm             =  1
  15 nstxout             =  50
  16 nstvout             =  1000
  17 nstfout             =  0
  18 nstlog              =  10
  19 nstenergy           =  10
  20 nstlist             =  10
  21 ns_type             =  grid
  22 deltagrid           =  2
  23 rlist               =  1.0
  24 rcoulomb            =  1.0
  25 rvdw                =  1.0
  26 ; Temperature coupling is on in two groups
  27 Tcoupl              =  yes
  28 tc-grps             =  Protein  SOL
  29 tau_t               =  0.1      0.1
  30 ref_t               =  300      300
  31 ; Energy monitoring
  32 energygrps          =  Protein  SOL
  33 ; Pressure coupling is not on
  34 Pcoupl              =  no
  35 tau_p               =  0.5
  36 compressibility     =  4.5e-5
  37 ref_p               =  1.0
  38 ; Generate velocites is on at 300 K.
  39 gen_vel             =  yes
  40 gen_temp            =  300.0
  41 gen_seed            =  173529