Dear All, while energy minimization with the protein fixed i am getting following error:
*t = 0.011 ps: Water molecule starting at atom 21089 can not be settled. Check for bad contacts and/or reduce the timestep.* Even if i am reducing timesteps its not working. The minim.mdp file which i have used is:; ntegrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm dt = 0.01 emstep = 0.01 ; Energy step size nsteps = 20000 ; Maximum number of (minimization) steps to perform constraints = all-bonds ; convert all bond to constraints ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1 ; Short-range electrostatic cut-off rvdw = 1 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) optimize_fft = yes pme_order = 4 fourierspacing = 0.15 ; Non-equilibrium MD stuff freezegrps = Protein Sol freezedim = Y Y Y N N N Regards, Prakash.
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