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On 6/04/2012 3:36 PM, Albert wrote:
<blockquote cite="mid:4F7E80E9.2020309@gmail.com" type="cite">
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<font size="+1"><font face="Arial">hello:<br>
<br>
thank you very much for your kind messages. I first did
minimization, the NVP with gradually heating the system from
0-310K, and them NPT production:<br>
<br>
----NVT.mpd---------------<br>
define = -DPOSRES -DPOSRES_LIG<br>
constraints = hbonds<br>
integrator = md<br>
dt = 0.001 ; ps !<br>
nsteps = 3000000 ; total 3000.0 ps.<br>
nstcomm = 10<br>
nstxout = 5000 ; collect data every 1.0 ps<br>
nstxtcout = 5000<br>
nstvout = 5000<br>
nstfout = 0<br>
nstlog = 10<br>
nstenergy = 50<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1.2<br>
coulombtype = PME<br>
rcoulomb = 1.2<br>
vdwtype = cut-off<br>
rvdw = 1.4<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
DispCorr = no<br>
; Berendsen temperature coupling is on<br>
Tcoupl = v-rescale<br>
tau_t = 0.1 0.1<br>
tc-grps = protein non-protein<br>
ref_t = 310 310<br>
; Pressure coupling is off<br>
Pcoupl = no<br>
Pcoupltype = isotropic<br>
tau_p = 1.0<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
pbc = xyz<br>
annealing = single single<br>
annealing_npoints = 2 2<br>
annealing_time = 0 5000 0 5000<br>
annealing_temp = 0 310 0 310<br>
gen_vel = no<br>
constraint_algorithm = Lincs<br>
<br>
<br>
---NPT md.mdp--------------------------<br>
constraints = hbonds<br>
integrator = md<br>
dt = 0.002 ; ps !<br>
</font></font></blockquote>
<br>
This time step is normally too long for those constraints. See
manual 6.5.<br>
<br>
<blockquote cite="mid:4F7E80E9.2020309@gmail.com" type="cite"><font
size="+1"><font face="Arial"> nsteps = 5000000 ; total
10ns.<br>
nstcomm = 10<br>
nstxout = 20000 ; collect data every <br>
nstenergy = 20000<br>
nstxtcout = 20000<br>
nstvout = 0<br>
nstfout = 0<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1.2<br>
coulombtype = PME<br>
rcoulomb = 1.2<br>
vdwtype = cut-off<br>
rvdw = 1.4<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
DispCorr = no <br>
; Berendsen temperature coupling is on<br>
Tcoupl = v-rescale<br>
tau_t = 0.1 0.1<br>
tc-grps = protein non-protein<br>
ref_t = 310 310<br>
; Pressure coupling is on<br>
Pcoupl = parrinello-rahman<br>
</font></font></blockquote>
<br>
Don't use algorithms that are known to be unstable for equilibration
while you are doing equilibration. See manual.<br>
<br>
<blockquote cite="mid:4F7E80E9.2020309@gmail.com" type="cite"><font
size="+1"><font face="Arial"> Pcoupltype = isotropic<br>
tau_p = 1.0<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
; Generate velocites is on at 310 K.<br>
gen_vel = yes<br>
</font></font></blockquote>
<br>
Why bother doing slow heating if you're just going to re-initialize
with random velocities again?<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:4F7E80E9.2020309@gmail.com" type="cite"><font
size="+1"><font face="Arial"> gen_temp = 310.0<br>
gen_seed = 6666<br>
<br>
</font></font> <br>
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