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