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 −Pxx−Pxx. 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.
It is important to consider the effect of water on your results as the pressure is computed for the whole system, including water molecules. This means that the deformation of the box will affect the water molecules as well, and the resulting pressure will be influenced by the water. To minimize this effect, you could try using a smaller box or reducing the number of water molecules in the system. Additionally, you may want to consider using a different type of barostat, such as the Berendsen or the isotropic Parrinello-Rahman barostat, to better control the pressure of the system during deformation. It is always a good practice to run simulations with different conditions and compare the results to determine the effect of different factors on the outcome.
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