Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~julia_p/pr5/md.mdp Дата изменения: Mon May 16 16:10:56 2011 Дата индексирования: Tue Oct 2 06:13:18 2012 Кодировка:

title = d_helix
cpp = /lib/cpp -traditional
constraints = all-bonds
unconstrained-start = yes
integrator = md
tinit = 0
dt = 0.001 ; ps !
nsteps = 50000 ; total 10 ps.
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 5
nstlist = 10
ns_type = grid
pbc = no;
lincs_iter = 4
; Long-range
coulombtype = Cut-off
vdwtype = Cut-off ;shift
rlist = 0 ;0.74 ; 11 A cut-off for ns
rvdw = 0 ;0.73 ; 10 A cut-off for vdw
rcoulomb = 0 ;0.74 ; 10 A cut-off for coulomb
; Berendsen temperature coupling is on in two groups
Tcoupl = no; V-rescale
tau_t = 0.1 ; 0.1 ; 0.1 0.1
tc-grps = System
ref_t = 300 ; 300 ; 300 300

; Isotropic pressure coupling is now on
Pcoupl = no; berendsen
Pcoupltype = isotropic
tau_p = 5
compressibility = 4.5e-5 ; 4.5e-4 4.5e-4 0 0 0
ref_p = 4.0 ;1.0 1.0 1.0 1.0 1.0

; Energy monitoring
energygrps = System
; Generate velocites is on at 300 K.
gen_vel = yes ;no

;freezegrps = System
;freezedim = Y Y N