GROMACS version: 2021
GROMACS modification: Yes
I have an infinite CG model of the material solvated in water. I am trying to apply a uniaxial deformation along a particular x-axis; the mdp settings in gromacs are below.
tcoupl = v-rescale
tc-grps = SOLID W_ION
tau_t = 1.0 1.0
ref_t = 298 298
Pcoupl = parrinello-rahman
Pcoupltype = anisotropic
tau_p = 12.0
compressibility = 0.0 3e-4 3e-4 0.0 0.0 0.0
ref_p = 0.0 1.0 1.0 0.0 0.0 0.0
deform = 0.002 0 0 0 0 0
Stress is computed as negative of the pressure tensor -P_{xx}. I wonder if water will affect my results, as I believe the Pressure is computed for the whole system. Previously, I used to pull one end of the model, keeping the other side fixed. Here, I am just pulling the box. Any suggestions? Thanks.