This is likely an embarrassingly trivial problem, but let's see. I am following the energy minimization scheme presented in the groningen tutorial
http://md.chem.rug.nl/education/mdcourse/MDpract.html I believe I follow the directions exactly, yet I can not minimize below Fmax~500 I download 1AKI, as in the tutorial, I issue pdb2gmx -f 1AKI.pdb grompp -f minim.mdp mdrun -v and I use the mdp file " title = Minimization of Hen Egg White Lysozyme (1AKI.pdb) ; Title of run ; The following lines tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor include = -I../top ; Directories to include in the topology format ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol nsteps = 200 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps = Protein ; Which coordinate group(s) to write to disk energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = no ; Periodic Boundary Conditions (yes/no)" I tried multiple choices of potentials and I tried gromacs 3.3.2, 3.3.3 and cvs, with single and double precision. They all finish with the same output(except single finishes in fewer steps) "Step= 57, Dmax= 3.2e-11 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478 Step= 60, Dmax= 9.6e-12 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478 Step= 62, Dmax= 5.8e-12 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478 Step= 65, Dmax= 1.7e-12 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478 Step= 67, Dmax= 1.0e-12 nm, Epot= -9.45085e+03 Fmax= 8.07834e+02, atom= 478 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1 writing lowest energy coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.5# Steepest Descents converged to machine precision in 68 steps, but did not reach the requested Fmax < 1. Potential Energy = -9.59521978368287e+03 Maximum force = 8.07834306442108e+02 on atom 478 Norm of force = 1.49469417798063e+02 " This seems unreasonably high. Are there some obvious mistakes people make that result in this kind of behavior? I have tried multiple pdb structure and none of them can minimize below fmax~100. I have also tried l-bfgs and cg. None of them can converge to the request precision. thanks -Paul
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