dear chris I did EM :
Steepest Descents did not converge to Fmax < 2000 in 101 steps. Potential Energy = -3.2421097e+05 Maximum force = 1.4766100e+04 on atom 1441 Norm of force = 2.5146213e+02 I am sure that constraints=none during EM. how do I increase the LINCS/SHAKE iterations to the appropriate number? this is my em.mdp file cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no
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