[gmx-users] Energy minimization error

[Mark Abraham]

Hi,

Look at atom 380 and see why the forces might be high.

Mark

On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <farideh.khamseh at gmail.com>
wrote:

> 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
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