- Posts: 5
Lipid bilayer tutorial - npt problem
- sajjad.ir
- Topic Author
- Offline
- Fresh Boarder
Less
More
6 years 8 months ago #7315
by sajjad.ir
Lipid bilayer tutorial - npt problem was created by sajjad.ir
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
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
Please Log in or Create an account to join the conversation.
- peterkroon
- Offline
- Gold Boarder
Less
More
- Posts: 210
6 years 8 months ago #7317
by peterkroon
Replied by peterkroon on 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
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
Please Log in or Create an account to join the conversation.
- sajjad.ir
- Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 5
6 years 8 months ago #7318
by sajjad.ir
Replied by sajjad.ir on 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
I did as you mentioned, 10ns simulation with 2fs timestep npt. It worked.
Thank you again
Please Log in or Create an account to join the conversation.
Time to create page: 0.090 seconds