I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density
when I create the box using genbox is 997.177g/l. I did energy
minimization run and the potential energy did converge smoothly, so I
did NPT equilibration run of 100ps and I got the density value of
975g/l. Why does the density decrease after the run? these are the
parameters that I used :
RUN CONTROL PARAMETERS
integrator = md
tinit = 0
dt = 0.002
nsteps = 50000
nstcomm = 0
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 0
xtc_precision = 1000
nstlist = 5
ns-type = Grid
pbc = xyz
rlist = 1.1
coulombtype = pme
rcoulomb = 1.1
epsilon-r = 1
vdw-type = switch
rvdw-switch = 0.8
rvdw = 1.0
Tcoupl = V-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
Pcoupl = berendsen
tau_p = 0.5
compressibility = 4e-05
ref_p = 1.0
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = no
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
Am I missing something?
Thanks
Nisha Patel
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