Error minimization of energy

User discussions
1

GROMACS version: 5.1.4
GROMACS modification: Yes/No
Here post your question
I am minimizing the energy of protein_ligand complex and getting the following error message.
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.40785e+21 Fmax= inf, atom= 5404
Step= 14, Dmax= 1.2e-06 nm, Epot= 1.40785e+21 Fmax= inf, atom= 5404
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.

Back Off! I just backed up em.gro to ./#em.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 1.4078480e+21
Maximum force = inf on atom 5404
Norm of force = inf
How to solve this error and complete energy minimization ? Any suggestions please

2

Hi,
you could try to increase the step-size emstep. You can also use single precision for this step.
I hope it helps
\Alessandra

3

Hi Alevilla,
I will try as per your suggestion.
Thanks

4

Your force is inf right from step 0. Check atom 5404 to see if it has exactly the same coordinates as some other atom. If not, do what gromacs suggested and try double precision em with all constraints off (including water via something like define=-DFLEXIBLE in your .mdp file). If so, (a) figure out what led to that and fix it or (b) adjust the coordinates of atom 5404 by the smallest amount you can and try again. If using option b, inspect your post-EM structure very carefully (it is likely to have some serious problems anyway).