[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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