regarding constant PH simulation

From: zahra nabavi (
Date: Thu Nov 19 2020 - 21:07:35 CST

Dear NAMD Community,

I have two questions regarding constant PH simulation.

1- I am planning to use it for a new molecule but as far as I know it only
works for aminoacids. What changes do I need to make so I could use it for
protonation of my own molecule? Is there any tutorial or guide to help me
make required changes to the TCL and input files?

2- When we change protonation states from protonated to deprotonated states
or vice versa, are there any "ghost" hydrogens somewhere in the system to
compensate for the movement of the charge between solvent and the
aminoacid? and if not, isn't it going to affect the PME calculations?

Thank you in advance,

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