[gmx-users] error while energy minimization with the protein fixed

[prakash verma]

Dear All,

while energy minimization with the protein fixed i am getting following
error:


*t = 0.011 ps: Water molecule starting at atom 21089 can not be settled.
Check for bad contacts and/or reduce the timestep.*
Even if i am reducing timesteps its not working.
The minim.mdp file which i have used is:;


ntegrator      = steep         ; Algorithm (steep = steepest descent
minimization)
emtol           = 1000          ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
dt              = 0.01
emstep          = 0.01          ; Energy step size
nsteps          = 20000         ; Maximum number of (minimization) steps to
perform

constraints     =  all-bonds    ; convert all bond to constraints
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist         = 5             ; Frequency to update the neighbor list and
long range forces
ns_type         = grid          ; Method to determine neighbor list (simple,
grid)
rlist           = 1             ; Cut-off for making neighbor list (short
range forces)
coulombtype     = PME           ; Treatment of long range electrostatic
interactions
rcoulomb        = 1             ; Short-range electrostatic cut-off
rvdw            = 1             ; Short-range Van der Waals cut-off
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
optimize_fft             = yes
pme_order                = 4
fourierspacing           = 0.15
; Non-equilibrium MD stuff
freezegrps               = Protein Sol
freezedim                = Y Y Y   N N N


Regards,
Prakash.
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