Dear All,
I am trying to simulate lipid-water system (340 POPE lipids & 6120 TIP4P
Waters), during the solvation by genbox, It also add the the water at the
interior of the bilayer. I removed those water molecules by my perl script. But
after removing these water molecules I have observed a zone between the lipid
head group and water. I tried to do small simulations (50 to250 ps) using
different pressure coupling but still I am not getting the structure which have
homogeneous arrangement of water over lipid head group. There is uneven
distribution of water across the bilayer. During this sort simulations position
restrain on lipid was applied.
I tried Isotropic, semiisotropic,anisotropic pressure coupling with the
following parameter, but no luck
Isotropic:
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1
semiisotropic:
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 2 2
compressibility = 0 4.5e-5
ref_p = 0 1.0
anisotropic:
Pcoupl = Berendsen
pcoupltype = anisotropic
tau_p = 10.0 10.0 10.0 0 0
0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p = 1.0 1.0 1.0 0 0
0
I also tried NVT Ensemble but no success till now. could some one give some
idea what parameters I should take to overcome this problem. I searched the
mailing list this problem discussed so many time suggestion was after sort
simulation (10-20 ps) water will arrange properly,but I am not able to get
proper arrangement of water molecules. please suggest me where I am doing
mistake.
Other parameters od the MDP file.
define = -DPOSRES_LIPID
integrator = md
dt = 0.002
nsteps = 25000
nstcomm = 1
nstxout = 1000
nstvout = 500
nstlog = 100
nstenergy = 100
nstxtcout = 500
xtc_precision = 1000
xtc_grps = POPE SOL
energygrps = POPE SOL
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.2
fourierspacing = 0.12
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
vdw-type = Cut-off
gen_vel = yes
gen_temp = 300
gen_seed = 173529
constraints = all-bonds
constraint_algorithm = lincs
unconstrained_start = no
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 30
Thanks in advance,
Alok_______________________________________________
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