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Time Step PAMAM dendrimer
- doa.hawamdeh
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9 years 4 months ago #4235
by doa.hawamdeh
Time Step PAMAM dendrimer was created by doa.hawamdeh
Dear GROMACS users:
I want to study the complexation between PAMAM dendrimer and DNA using coarse-graining molecular dynamics simualtions (MARTINI force field) utilizing GROMACS version 5.0.3.
MD integrator is used with time step of 20 fs, but I could not run the simulation with this time step, I got segmentation fault. Sure before running long simulation I minimized the system. Below is the .mdp file that I used. Could you please help me?
Waiting your response.
Thank you.
integrator = md
dt = 0.02
nsteps = 5000000
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
nstlist = 10 ; 10 fs
ns_type = grid ; search neighboring grid cells
pbc = xyz
rlist = 1.4 ; short-range neighborlist cutoff (in nm)
coulombtype = shift ; Particle Mesh Ewald for long-range electrostatics
;fourierspacing = 0.15 ; grid spacing for FFT
;pme_order = 4 ; cubic interpolation
;optimize_fft = yes
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = shift
rvdw_switch = 0.9
rvdw = 1.2
;ewald_rtol =1e-5
tcoupl = berendsen
tc-grps = System
tau_t = 1.0
ref_t = 310
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = no
gen_temp = 310
gen_seed = 473529
cutoff-scheme =group
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
;lincs_order = 4
;lincs_warnangle = 30
I want to study the complexation between PAMAM dendrimer and DNA using coarse-graining molecular dynamics simualtions (MARTINI force field) utilizing GROMACS version 5.0.3.
MD integrator is used with time step of 20 fs, but I could not run the simulation with this time step, I got segmentation fault. Sure before running long simulation I minimized the system. Below is the .mdp file that I used. Could you please help me?
Waiting your response.
Thank you.
integrator = md
dt = 0.02
nsteps = 5000000
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
nstlist = 10 ; 10 fs
ns_type = grid ; search neighboring grid cells
pbc = xyz
rlist = 1.4 ; short-range neighborlist cutoff (in nm)
coulombtype = shift ; Particle Mesh Ewald for long-range electrostatics
;fourierspacing = 0.15 ; grid spacing for FFT
;pme_order = 4 ; cubic interpolation
;optimize_fft = yes
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = shift
rvdw_switch = 0.9
rvdw = 1.2
;ewald_rtol =1e-5
tcoupl = berendsen
tc-grps = System
tau_t = 1.0
ref_t = 310
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = no
gen_temp = 310
gen_seed = 473529
cutoff-scheme =group
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
;lincs_order = 4
;lincs_warnangle = 30
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- helgi
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- Posts: 54
8 years 5 months ago #5158
by helgi
Replied by helgi on topic Time Step PAMAM dendrimer
The Martini DNA is rather unstable - depending on the version you are using and if you are using the soft/stiff elastic network. In most cases you should be able to run at 10 fs, but 20 fs is most likely too large.
Cheers,
- Helgi
Cheers,
- Helgi
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