GROMACS version:2022.3
i am making box of 1m trehalose using charmm force field during neutralization i encounter this warning , in previous discussions i see they suggest to change gromacs using older version ,i do that after that also i encounter same problem in minimization,i also increase cut off but not work.
WARNING 2 [file ions.mdp]:
The largest distance between excluded atoms is 7.247 nm, which is larger
than the cut-off distance. This will lead to missing long-range
corrections in the forces and energies. If you expect that minimization
will bring such distances within the cut-off, you can ignore this warning.
i ignore this warning by puttiong -maxwarn 2 but when i do minimization i encounter this problem
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.
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 6.9622080e+15
i am attatching my em_steep.mdp file
Input file^M
;^M
cpp = /usr/bin/cpp^M
define = -DFLEX_SPC^M
constraints = h-bonds
integrator = steep
nsteps = 3000^M
;
; Energy minimizing stuff
;
emtol = 1000^M
emstep = 0.01^M
nstcomm = 100^M
cutoff-scheme = Verlet
ns_type = grid^M
rlist = 0.9^M
coulombtype = PME^M
rcoulomb = 1.4^M
rvdw = 1.4^M
fourierspacing = 0.12^M
fourier_nx = 0^M
fourier_ny = 0^M
fourier_nz = 0^M
pme_order = 4^M
ewald_rtol = 1e-5^M
optimize_fft = yes^M
Tcoupl = no^M
Pcoupl = no^M
gen_vel = no^M
~
also i try by changing emtol to 1500 and rlist to 1.4 but still same error persist.