Dear All,
I am new to MD simulation world, and I am doing protein simulation with different salt. I was wondering if I could add NaPO4 as the ions to neutralize the system instead of using NA+ and CL+. I would appreciate if any friends can give me some hints, thank you very much.
Jamoliddin Razzokov
Jery Lee
Ions such as Na and CL are in the database of the gromacs, therefore, you can add them by means of commands. I don't know for the case of PO4. Maybe it would be possible if you can add PO4 parameters to the ions.itp in the database.The next easiest option: first add NaCL using the standard command genion. Next, using the insert molecules command you can replace CL ions with PO4 in the system.
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