Hi,I am studying the toxicity effect of ZnO nanoparticle (with a partial charges of +1.026 and -1.026 for Zinc and Oxygen atoms, respectively) on the Albumin structure by Gromacs. For MD simulation the nanoparticle was placed at a distance of 1nm of protein, after running pdb2gmx, the simulation box was solvated by TIP3P waters. The net charge of protein in physiological condition is -14 that was neutralized by adding sodium and chloride ions to box. Then, energy minimization, NVT and NPT were done. From the beginning of md simulation, the protein structure began to be unfolded slowly before binding nanoparticle to it and after binding, the protein structure changed dramatically. I cannot consider the charge of ZnO as zero like silver or gold nanoparticles. So, I am confused that whether the study method is correct or wrong for this interaction? Do the results seem logical? Thanks
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