GROMACS version: 2024.3
After energy minimization step, part of the protein structure breaks and goes to the other side of the box. How do i solve this?
My mdp file is
integrator = steep
emtol = 1000.0
emstep = 0.01
nsteps = 50000
nstlist = 1
cutoff-scheme = Verlet
ns_type = grid
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
I did try using -DPOSRES, reduced emstep to even further like 0.001/0.0001 still it breaks. The structure looks perfectly fine before EM.