
Input files related to the publication:

How does protein protonation change upon crystallization: 
insights from constant pH molecular dynamics simulations
by Noora Aho, Gerrit Groenhof and Pavel Buslaev (2024)

crystal_setup/ 

	The system with protein crystal was setup using the gmXtal tool:
	python gmxtal.py -m prep -c config.yaml 
	
	-> will create the input structure and script for running 
	more details about gmXtal in https://gitlab.com/pbuslaev/gmxtal
	
titration_crystal/

	Start from the equilibrated crystal (output of gmXtal script) and 
	create gromacs input files for constant pH using the phbuilder tool:
	
	- important: add A/B chain labels to the .pdb file for separate crystal 
	             entities to prevent them being connected
	phbuilder gentopol -f 6_npt.pdb -ph 7.0
	phbuilder neutralize -f phprocessed.pdb -nbufs 80 -solname HOH 
	(adjust the number of buffers accordingly)
	phbuilder genparams -f phneutral.pdb -ph 7.0 
	-> run em, nvt and npt and md at different pH values for titration 
	more details about phbuilder in https://gitlab.com/gromacs-constantph/phbuilder/
	and constant ph MD in gromacs in general in https://gitlab.com/gromacs-constantph/constantph 
	
titration_solution/

	Start from the .pdb structure of the protein and run phbuilder as for the crystal, 
	following the basic workflow in https://gitlab.com/gromacs-constantph/phbuilder/
	-> run em, nvt and npt and md at different pH values for titration 


