Uniaxial Elongation to get tensile stress vs. tensile strain curve

User discussions
1

GROMACS version: 2021
GROMACS modification: No
Here post your question

I am trying to obtain the tensile stress–strain curve for a polymer by performing uniaxial elongation in the z-direction. Below is the .mdp file with the input parameters. Since the elongation is applied along the z-direction, I expect the pressure to increase in z, while the x and y directions should maintain constant pressure. However, what I observe is that the pressure remains the same in all three directions. As a result, the stress–strain plot I obtain is flat. I have attached the plot below. Could you please help me understand where I might be going wrong?

title = OPLS
integrator = md
nsteps = 5000000
dt = 0.002
; Output control
nstenergy = 5000
nstlog = 5000
nstxout-compressed = 5000
compressed-x-grps = System
; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = h-bonds
lincs_iter = 1
lincs_order = 4
; Nonbonded settings
cutoff-scheme = Verlet
ns_type = grid
nstlist = 10
rcoulomb = 1.0
rvdw = 1.0
DispCorr = EnerPres
; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
; Temperature coupling is on
tcoupl = V-rescale
tc-grps = system
tau_t = 0.1
ref_t = 300
; Pressure coupling is on
pcoupl = Berendsen
pcoupltype = semiisotropic
tau_p = 1.0
ref_p = 1.0 0.0
compressibility = 4.5e-5 0.0
deform = 0.0 0.0 0.0005 0.0 0.0 0.0
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = no ; Velocity generation is off

image
image1255×889 32.8 KB

2

The pressure should decrease, not increase, along z. It seems to do that a bit. But if you system is liquid, there will be no pressure change at all.

3

Thanks hess for the reply. Even if the pressure should decrease in z-direction, the stress strain plot should not be flat. My system contains only 100chains of 10mer length polymer. Can you please let me know if any changes need to be done in .mdp file.

4

I don’t know how your system looks like. As I wrote, if your polymer melt is liquid, you will never get a stress. If it is in a glass or solid phase, you should.

5

Dear Hess,

The polymer melt is in solid phase. In this case, could you please help me understand the possible reason for observing a constant pressure in the z-direction instead of a decreasing trend? Also, do I need to make any modifications in the .mdp file to address this?