Energy minimization error

GROMACS version: 2020-3
GROMACS modification: No

Dear all,

Hello, my name is Tiara. I am new to Gromacs and molecular dynamic. I am trying to do a simulation to a protein complexed with ligand. When I tried to minimizing energy [gmx mdrun -v -deffnm EM -nt 1], I got this following error:

Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= -6.34945e+05 Fmax= 1.91991e+05, atom= 2089
Step= 14, Dmax= 1.2e-06 nm, Epot= -5.08151e+05 Fmax= 2.31330e+05, atom= 2742
Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (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.2#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -6.3494538e+05
Maximum force = 1.9199108e+05 on atom 2089
Norm of force = 4.5047012e+03
.
.
.
And here’s my em.mdp file:
integrator = steep ; Algorithm (steep = steepest descent minimization)
dt = 0.002 ; Energy step size
nsteps = 5000 ; Maximum number of (minimization) steps to perform

nstenergy = 5000
nstxout-compressed = 5000

continuation = yes
constraints = none

cutoff-scheme = Verlet

coulombtype = PME
rcoulomb = 1.0
DispCorr = EnerPres

tcoupl = V-rescale
tc-grps = Protein SOL
tau-t = 0.1 0.1
ref-t = 300 300

pcoupl = Parrinello-Rahman
tau-p = 2.0
compressibility = 4.5e-5
ref-p = 1.0

I have tried for months and got no result… I have attached my files below. I would appreciate a lot if somebody could help me to fix this problem. I have no one to ask but here… Please… Thank you so much…

I’m doing it on 673 protein residues, 1 other residues, 23494 water residues, and 122 ion residues. Here’s my box info(s):
Read 10836 atoms
Volume: 400.96 nm^3, corresponds to roughly 180400 electrons
No velocities found
system size : 6.328 6.889 9.197 (nm)
center : 4.544 6.872 4.662 (nm)
box vectors : 6.328 6.889 9.197 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume : 400.96 (nm^3)
shift : -0.380 -2.427 0.937 (nm)
new center : 4.164 4.445 5.599 (nm)
new box vectors : 8.328 8.889 11.197 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 828.89 (nm^3)

Dr. Lemkul’s tutorial has nice explanation about energy minimization. Though it is not problem, but your mdp file contains some redundant options, e.g. thermostat and barostat option. Please collect a clean mdp file from the tutorial. There are few things that you might want to try,

  • Decrease step size of minimization search (emstep)

  • Try different minimization algo (e.g.: cg, l-bfgs)

  • Try double precision version of gromacs, sometimes useful for accurate gradient calculations.

  • Try slightly larger box, as you have very high force on atoms.

  • It is worth rechecking your force field parameters and connectivities

Regards
Masrul

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http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#stepsize-too-small-or-no-change-in-energy-converged-to-machine-precision-but-not-to-the-requested-fmax

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Dear, Sir Masrul.

Thank you so much for the reference and the link, it worked for me. Thank you, Sir.

Regards,
Tiara.

Dear Dr DBW.

Thank you for the reference. I’ve read it and my problem solved by changing the minim.mdp file. Thank you for answering.

Regards,
Tiara.

Hello Tiara,

Can you clearly tell what change you made in the em.mdp file as I am also facing the same issue and not able to proceed for the past 2 months
I am new to simulation
Kindly help…
I changed the algorithm to CG but didnt work…