Justin,
I've forced with the problem that I could not prorerly minimized my system in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot value lower than +3.00 with that parametries ( I've used KALP peptide as a test input ) ; Parameters describing what to do, when to stop and what to save integrator = steep emtol = 1 ; Stop minimization when the maximum force < 1.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5000000 ; 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 ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = Shift rcoulomb = 1.0 rcoulomb_switch = 0.0 vdwtype = Shift rvdw = 1.0 rvdw_switch = 0.0 Than I've tried to futher minimized this structure via l-bfgs algorithm by integrator = l-bfgs dt = 0.01 emtol = 0.001 ; emstep = 0.1 ; Energy step size nsteps = 50000000 ; Maximum number of (minimization) steps to perform but Epot was still big. What I've done wrong ?
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