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I'm doing a dynamic of a peptide in a mixture TFE/H2O ( 30/70 %).<BR>
I'm using this file.mdp :<BR>
<BR><FONT size=2>
cpp = /lib/cpp<BR>
define = -DFLEX_SPC -DPOSRES<BR>
constraints = all-bonds<BR>
integrator = md<BR>
tinit = 0.0<BR>
dt = 0.002 ; ps !<BR>
nsteps = 500000 ; total 1000 ps.<BR>
nstcomm = 1<BR>
nstxout = 1000<BR>
nstvout = 1000<BR>
nstfout = 0<BR>
nstxtcout = 50<BR>
xtc_precision = 1000<BR>
nstlog = 1000<BR>
nstenergy = 1000<BR>
nstlist = 5<BR>
rlist = 1.0<BR>
coulombtype = Cut-off<BR>
rcoulomb = 1.4<BR>
rvdw = 1.4<BR>
epsilon_r = 1.0<BR>
; Temperature coupling is on in two groups<BR>
Tcoupl = Berendsen<BR>
tc-grps = system<BR>
tau_t = 0.1<BR>
ref_t = 300<BR>
; Energy monitoring<BR>
energygrps = system<BR>
; Pressure coupling is not on<BR>
Pcoupl = Berendsen<BR>
tau_p = 0.5<BR>
compressibility = 4.5e-5<BR>
ref_p = 1.0<BR>
; Generate velocites is on at 300 K.<BR>
gen_vel = no<BR>
gen_temp = 300<BR>
gen_seed = 173529<BR>
<BR>
<BR>
<BR>
I 'd know if this file is correct.<BR>
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