Hi everyone,
I try to simulate a system for the interaction of Ti2C and Nb2C two-dimensional monolayers with an organic molecule using gromacs. The considered monolayers are periodic structures in x-y direction in triclinic boxes. I face with two challenges:
First, I use “gmx editconf -f MXene.pdb -o MXene.gro -box 4 4 5 -angles 90 90 120” to insert monolayers in their triclinic boxes. Then, I use “gmx solvate -cp MXene.gro -cs spc216 -o MXene-solv.gro” to add water solvent. But, the water molecules were added as a cubic instead of triclinic box. The attached image displays this system.
Second:
Based on the published papers, I want to use OPLS-AA force field for studying this interactions. But, finding force field parameters for Ti2C and Nb2C monolayers is unsuccessful for me. Can anyone help me to find or construct related .itp files for these simulations? If it possible, sharing a link or clear manual will be helpful for me.