[gmx-users] Minimization problem

Neda Rafiee nerafiee at ipm.ir
Tue Jan 9 23:45:47 CET 2018

Dear Users,
I have a problem in energy minimization step. Actually I have some groups of atoms that are freezed and also a chain of protein in water. I want the following items:
constraints         =  none
integrator          =  steep
emstep              =  0.0001
emtol               =  500.0
nsteps              =  500000
; Neighbor list and pbc's ------------------------------------------
cutoff-scheme       =  group
nstlist             =  1        ; default is 10 -- try more frequent
ns_type             =  grid     ; simple (for no pbc) or grid
pbc                 =  xyz      ; CHANGE
periodic_molecules  =  no
; Interaction parameters -------------------------------------------
rlist               =  1
rlistlong           =  1
rcoulomb            =  1
coulombtype         =  PME
epsilon_r           =  1
vdwtype             =  user; cut-off
rvdw                =  1 

but after just 6000 steps it gives me this error:
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 500 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 53429 steps,
but did not reach the requested Fmax < 500.
Potential Energy  =  2.46705107676305e+14
Maximum force     =  9.69602643026733e+08 on atom 9415
Norm of force     =  1.70746371816015e+07

Would you please help me understand where the problem is ?!

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