Justin,<br><br><br>I've forced with the problem that I could not prorerly minimized my system in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot value lower than +3.00 with that parametries ( I've used KALP peptide as a test input )<br>
<br>; Parameters describing what to do, when to stop and what to save<br>integrator = steep <br>emtol = 1 ; Stop minimization when the maximum force < 1.0 kJ/mol/nm<br>emstep = 0.01 ; Energy step size<br>
nsteps = 5000000 ; Maximum number of (minimization) steps to perform<br><br><br><br>; 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 = 1.2 ; Cut-off for making neighbor list (short range forces)<br>coulombtype = Shift <br>rcoulomb = 1.0<br>
rcoulomb_switch = 0.0<br>vdwtype = Shift<br>rvdw = 1.0<br>rvdw_switch = 0.0 <br><br>Than I've tried to futher minimized this structure via l-bfgs algorithm by <br><br>integrator = l-bfgs<br>
dt = 0.01 <br>emtol = 0.001 ;<br>emstep = 0.1 ; Energy step size<br>nsteps = 50000000 ; Maximum number of (minimization) steps to perform<br><br>but Epot was still big.<br>
<br>What I've done wrong ?<br>