<div>I am doin the first minimization step.. here are the details of minim.mdp file</div>
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<div>; minim.mdp - used as input into grompp to generate em.tpr<br>; Parameters describing what to do, when to stop and what to save<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>
emstep = 0.01 ; Energy step size<br>nsteps = 50000 ; Maximum number of (minimization) steps to perform</div>
<div>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>nstlist = 1 ; Frequency to update the neighbor list and long range forces<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)<br>coulombtype = PME ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.0 ; Short-range electrostatic cut-off<br>rvdw = 1.0 ; Short-range Van der Waals cut-off<br>
pbc = xyz ; Periodic Boundary Conditions (yes/no)</div>
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