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…