[gmx-users] Freeze-Exclude a molecule

[Sajjad Kavyani]

Dear experts,
I want to simulate a system with a cnt and a molecule passing through it by
a coarse grained ff.
First, I ran a nvt (after an em) for a single molecule (no solvent) with no
problem.
Second, I do the same with a single cnt and absolutely no problem.
The problem is where I put them together in a single box. Every time I
tried that, the "segmentation fault" appears.
Even in a very large box of 60 nm!!, where they barely see each other to
interact.
NOTE: The system has zero charge.

Could someone please explain the situation for me?

The MDP parameter is :

integrator               = md
tinit                    = 0.0
dt                       = 0.020
nsteps                   = 102000
nstcomm                  = 1

nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 0
nstlog                   = 1000
nstenergy                = 1000
nstxtcout                = 1000
xtc_precision            = 1000
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.2
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
rvdw_switch              = 0.9
rvdw                     = 1.2
DispCorr                 = No
tcoupl                   = berendsen
tc-grps                  = system
tau_t                    = 1.0
ref_t                    = 300
Pcoupl                   = no
compressibility          = 1e-5
gen_vel                  = no
gen_temp                 = 320
gen_seed                 = 473529
constraints              = none
constraint_algorithm     = Lincs
unconstrained_start      = no
lincs_order              = 4
lincs_iter              = 1
lincs_warnangle          = 90