Dear Users,
I conducted uniaxial deformation simulations (in the z-direction) for my polymer systems to investigate the changes in Young’s modulus of the polymer with additives. Please see the .mdp options I used for the simulation below. However, I noticed that my polymer moved to the middle of the box after 10 ns of deformation simulation, and the box dimensions extended due to stretching in the z-direction. However, I observed void volumes throughout most of the simulation box without significant changes in the polymer.
I would like to know whether I need to apply position restraints in my simulations to better observe the polymer’s deformation.
Thank you.
integrator = md
nsteps = 6000000
dt = 0.002
nstlist = 20
ns_type = grid
nstlog = 50000
nstenergy = 50000
nstxtcout = 50000
xtc_precision = 50000
continuation = yes
constraint_algorithm = lincs
constraints = hbonds
cutoff-scheme = Verlet
rcoulomb = 1.2
rvdw = 1.2
coulombtype = PME
pme_order = 8
fourierspacing = 0.12
tcoupl = v-rescale
tc-grps = System
tau_t = 0.100000
ref_t = 310.0
nsttcouple = 5
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 1.0
ref_p = 1.0 0
compressibility = 4.5e-5 0
refcoord_scaling = com
pbc = xyz
DispCorr = EnerPres
gen_vel = no