*Dear all, I am trying to minimize the energy of the single molecule using gromacs. I tried with the following mdp
; VARIOUS PREPROCESSING OPTIONS FOR ENERGY MINIMIZATION OF ISOLATED MOLECULE include = define = ; RUN CONTROL PARAMETERS integrator = steep nsteps = 5000 init_step = ; ENERGY MINIMIZATION OPTIONS emtol = 10 emstep = 0.01 nstcgsteep = nbfgscorr = nstcheckpoint = 100 nstlog = 100 nstenergy = 1 ; SIMULATED ANNEALING annealing = no annealing_npoints = annealing_time = annealing_temp = But it shows the following error, ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. I have not included any the cut-off in the mdp file, but it still shows the error. Am I supposed to include something to mdp to run single molecule energy minimisation. Thank you* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.*
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