[gmx-users] Energy minimization error

[faride badalkhani]

Thank you for your great help on specbond.dat file. I defined it and I
could go ahead until Energy minimization step. I have used this minim.mdp
file

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator    = steep        ; Algorithm (steep = steepest descent
minimization)
emtol          = 1000.0      ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep       = 0.01          ; Energy 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
ns_type           = grid        ; Method to determine neighbor list
(simple, grid)
rlist                 = 1.0        ; Cut-off for making neighbor list
(short range forces)
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 (yes/no)

But when I run mdrun -v -deffnm em command, I get this error:

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 90 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -2.3956744e+05
Maximum force     =  1.5824519e+05 on atom 380
Norm of force     =  1.7695243e+03

gcq#187: "Been There, Done It" (Beavis and Butthead)

farideh at farideh-P61A-D3:~/FARIDEH$

I changed the emtol, emstep, and nsteps for a few times. However, I
couldn't resolve this problem. Could you tell me if there is something
wrong with the minim.mdp file?

You can see all the files via:
https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0

Truly yours,
Farideh