REMD MDP文件

; Run control
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  5000000; total 10 ns.


; Output control
nstxout             =  100
nstvout             =  100
nstfout             =  100
nstlist             =  10
nstlog              =  100
nstenergy           =  100


; Neighbor searching
cutoff-scheme       = group
rlist               =  5
pbc                 =  no
ns_type             =  simple


; Electrostatics and VdW
rvdw            = 5
rcoulomb            = 5
coulombtype            = cut-off
vdwtype                    = cut-off


;Langevin dynamics
bd_fric             =  0
ld_seed             =  -1


; Bonds
constraints         = all-bonds
lincs_order         = 4
lincs_iter          = 1
lincs-warnangle     = 30


; Temperature and Pressure coupling
Tcoupl              = v-rescale
tau_t               = 1.0
tc-grps             =  Protein
ref_t               =  300
Pcoupl              =  no


; Velocity generation
gen_vel             =  yes
gen_temp            =  300
gen_seed            =  173529
;http://www.mail-archive.com/gmx-users@gromacs.org/msg20866.html


;mine addition
comm_mode        = angular
nstcomm                = 10


; IMPLICIT SOLVENT ALGORITHM
implicit_solvent         = gbsa


; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm             = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii               = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                 = 5
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent       = 80
; Salt concentration in M for Generalized Born models
gb_saltconc              = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha             = 1
gb_obc_beta              = 0.8
gb_obc_gamma             = 4.85
gb_dielectric_offset     = 0.009
sa_algorithm             = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension       = -1