Hi all,

I am trying to do molecular dynamics simulations in Discover module with some polymer molecules with caboxyl containing substituents (i.e., with the monomers of the type R-COOH). The carboxyl group needs to be in a deprotonated state (R-COO- and H+ separate). I did create this by setting the overall charge to R-COO- to -1 and that of proton (H+) to be +1 from Modify->Charges->Edit. The construction and packing tasks in Amorphous cell runs fine and shows that the system is overall neutral. However, when I do a NPT molecular dynamics run using Discover, my system keeps expanding to unphysical dilute concentrations. I tried disabling the automatic charge assignment in Discover setup to make sure if the partial charges are not re-assigned during the simulation but to not avail. I have also tried to create R-COOH by deleting the O-H bond while keeping the partial charges of R-COO- and H+ unchanged; it does not help either. Any suggestions?

Thanks,

Prateek