the energy minimisation step is not getting negative. I decrease emtol to 100 but it seems that this cannot occur. It stopped with the following description. I tried with another pdb of the same molecule and it’s still the same. Can I remove emtol in the script and only perform EM for like 10000 steps? Please let me know how to proceed. Thank you.
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (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)
It may be because of bad inititial structure, or mdp settings; you can play around it and finish the minimisation but it may not stabilise during equilibration and production. It would be better to provide more informations such as your simulations sytem and how you built it. Also i have seen a lot of questions on such issues in the past and searching on forum will definitly help you to get more on the issues;
; 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 = 100.0 ; Stop minimization when the maximum force < 10.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 10000 ; 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
cutoff-scheme = Verlet ; Buffered neighbor searching
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1 ; Short-range electrostatic cut-off
rvdw = 1 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
vdw-modifier = Potential-shift
I will try again with a modified structure. Please let me know if you see any changes that should be made to this file. Thank you.
The .mdp looks alright, but try to look at the structure in the vicinity of the highest-force atom. gmx mdrun usually tells you which atom experiences the highest forces, and often it’s only by looking at the problem with a pair of eyes that you can understand what went wrong.
I don’t understand where to find the info regarding the atom with the highest forces. Is it in the em.log file? I don’t see it there after minimisation. Thank you.