<table cellspacing='0' cellpadding='0' border='0' ><tr><td style='font: inherit;'>Hi all,<br>
<br>
In the TIP4P water layer above my dmpc bilayer after 100ps
(OPLS-BERGER) a hole is being formed. Some water molecules are absent
in the water layer, but the total no of water molecules are same. This
is my semi.mdp file<br>
<br>
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<pre>title = bilayer MD DMPC PURE
cpp = /usr/bin/cpp
define = -DDMPC_POSRES
constraints = all-bonds
constraint_algorithm= lincs
lincs_order = 4
lincs_warnangle = 30
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000 ; total 1 ns.
nstcomm = 1
comm-mode = linear
nstxout = 500
nstvout = 500
nstfout = 500
nstenergy = 100
nstlist = 5
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.4
pbc = xyz
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
coulombtype = PME
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = DMPC SOL
ref_t = 300 300
; Pressure coupling is not on
Pcoupl = berendsen
tau_p = 5.0 5.0
compressibility = 4e-5 4.5e-5
ref_p = 1.0 1.0
pcoupltype = semiisotropic
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
</pre>
awaiting your help<br><br><br>
</td></tr></table><br>
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