normal Lipid bilayer tutorial - npt problem

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2 months 2 days ago #7315 by sajjad.ir
sajjad.ir created the topic: Lipid bilayer tutorial - npt problem
Hi,
Recently I started the lipid bilayer tutorial.
I utilized the insane.py script in order to make a suitable initial structure for the lipid bilayer (DOPC) system (25x25x9 nm^3).
After a successful EM (with minimum force 5!) and NVT (for about 5ns), on the insane.py output, the system blows up in the NPT stage with some of :
" Warning: pressure scaling more than 1%, mu: 0.478451 0.478451 0.478451"
and then core dump!
the NVT and NPT systems both have position restrained (force 1000).

Could you please help me in order to find a solution? or tell me where is the problem

In the following, the NPT parameters are listed:
(both the PME and cut-off method for coulombic interaction were tested)

NPT parameters:

define =-DPOSRES
integrator = md
tinit = 0.0
dt = 0.020
nsteps = 5020000
nstcomm = 1
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 1000
off
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = cut-off ;PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = switch ;shift ;
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = berendsen
tc-grps = system
tau_t = 1.0
ref_t = 310
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = no
gen_temp = 320
gen_seed = 473529
handled
constraints = none ;all-bonds
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 30

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2 months 19 hours ago #7317 by peterkroon
peterkroon replied the topic: Lipid bilayer tutorial - npt problem
Hi,

I expect 5ns to be way too short. Also, you should probably use a semi-isotropic pressure coupling.
With what timestep did you run your NVT equilibration? Have you tried gently equilibrating your bilayer with a smaller timestep (1-10fs) like the tutorial recommends?
What positions do you have restrained? Why?

Peter

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2 months 14 hours ago #7318 by sajjad.ir
sajjad.ir replied the topic: Lipid bilayer tutorial - npt problem
Thanks Peter for your reply
I did as you mentioned, 10ns simulation with 2fs timestep npt. It worked.
Thank you again

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