Could anyone help me to solve the following error during energy minimization in GROMACS
Step=10343, Dmax= 1.8e-05 nm, Epot= 2.99234e+06 Fmax= 4.45471e+04, atom= 14522
Step=10348, Dmax= 1.4e-06 nm, Epot= 2.99234e+06 Fmax= 3.73969e+04, atom= 14522
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (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.
Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
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 10349 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 2.9923410e+06
Maximum force = 4.4547062e+04 on atom 14522
Norm of force = 3.4612451e+02
minim.mdp file is
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
define = -DPOSRES_LIPID
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
I pack this bilayer by using packmol, and added the upper slap and lower slap of water in gromacs, to avoid the water from a bilayer core. during minimization above arror is comming.
This is the initial bilayer
After minimization
