<b>Dear all,<br> I am trying to minimize the energy of the single molecule using gromacs. I tried with the following mdp <br><br>; VARIOUS PREPROCESSING OPTIONS FOR ENERGY MINIMIZATION OF ISOLATED MOLECULE<br>include =<br>
define =<br><br>; RUN CONTROL PARAMETERS<br>integrator = steep<br>nsteps = 5000<br>init_step =<br><br>; ENERGY MINIMIZATION OPTIONS<br>emtol = 10<br>
emstep = 0.01<br>nstcgsteep =<br>nbfgscorr =<br>nstcheckpoint = 100<br>nstlog = 100<br>nstenergy = 1<br><br>; SIMULATED ANNEALING<br>
annealing = no<br>annealing_npoints =<br>annealing_time =<br>annealing_temp =<br> <br>But it shows the following error,<br> ERROR: The cut-off length is longer than half the shortest box vector or<br>
longer than the smallest box diagonal element. Increase the box size or decrease rlist.<br><br> 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.<br>
<br><br>Thank you</b><br> <br><b>With Regards,<br>Ravi Kumar Venkatraman,<br>IPC Dept., IISc,<br>Bangalore, INDIA.<br><br><span style="color: rgb(0, 102, 0);">+91-9686933963.</span></b><br><br>