[gmx-developers] freeze group not working in implicit solvent

Javaria ashraf jia_ashraf at yahoo.com
Thu Mar 10 05:39:22 CET 2016


hello and good day all
i have a problem related to freeze groups. I have put some residues of protein in freeze group. They are located at different locations but I have put them in one freeze group. Is it okay? and I have used following mdp file:
integrator	= steep		; Algorithm (steep = steepest descent minimization)
emtol		= 100.0  	; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps		= 500	  	; Maximum number of (minimization) steps to perform
;continuation	= yes		
freezegrps      = bothCA
freezedim       = Y Y Y 
constraints	= none	
ns_type		= grid		
nstlist		= 1.0		
rlist		= 1.0		
rcoulomb	= 1.0		
rvdw		= 1.0		
coulombtype	= Cut-off	
pme_order	= 4		
fourierspacing	= 0.16		
tcoupl		= V-rescale	
tc-grps		= system ; i have changed it
tau_t		= 0.1 	
ref_t		= 300 
pbc		= xyz		
gen_vel		= no		
ld_seed 	= -1
implicit_solvent = GBSA
gb_algorithm     = OBC
nstgbradii       = 1.0
rgbradii	 = 1.0
gb_epsilon_solvent = 80
gb_dielectric_offset = 0.009
sa_algorithm   	     = Ace-approximation
sa_surface_tension   = 0.0054
but there is some movement in atoms belonging to freeze group. please help me out.
I have applied distance restraint and position restraint as well but nothing working properly. please suggest and point out where i am going wrong.
thanks in advance.
regards 
JIA


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