Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~golovin/pep_melt/md.mdp Дата изменения: Thu Mar 31 17:09:05 2016 Дата индексирования: Sun Apr 10 07:52:49 2016 Кодировка:

title = MD
cpp = /lib/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 10000000 ; total 1.0 ps.
nstcomm = 1
nstxout = 50000
nstvout = 50000
nstxtcout = 5000
;xtc-grps = System
nstfout = 0
nstlog = 1000
nstenergy = 10000
nstlist = 10
ns_type = grid
coulombtype = pme
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = v-rescale
tau_t = 0.1 0.1 ; 0.1 ; 0.1
tc-grps = Protein non-Protein
ref_t = 350 350 ; 350;300
; Pressure coupling is not on
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 5
compressibility = 4.5e-5; 4.5e-5 4.5e-5 0 0 0
ref_p = 1.0 ;1.0 1.0 1.0 1.0 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529