[gmx-users] Mplecular Dynamic simulation of DNA and PAMAM dendrimers

[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 use. 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
;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