Hi! Thanks a alot for all the suggestions i've got from Justin and Mark. <br>I found out that i actually deleted the box information from the starting structure PDB. Once i put it back, It worked. However,<br>it stopped with this message.<br>
<br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>
but not to the requested precision Fmax < 1000<br>You might need to increase your constraint accuracy, or turn<br>off constraints alltogether (set constraints = none in mdp file)<br><br>writing lowest energy coordinates.<br>
<br>Back Off! I just backed up em.trr to ./#em.trr.19#<br><br>Back Off! I just backed up em.gro to ./#em.gro.11#<br><br>Steepest Descents converged to machine precision in 76 steps,<br>but did not reach the requested Fmax < 1000.<br>
Potential Energy = -2.24796600790506e+05<br>Maximum force = 1.14539522791599e+03 on atom 6619<br>Norm of force = 1.62353061702859e+04<br><br>Is it mean that the minimization is done and is already converged?<br>
Here the result for the final Step 75.<div class="im"><br><br>Energies (kJ/mol)<br> Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih.<br></div> 1.23491e+03 9.85552e+03 4.48086e+03 4.81663e+03 1.33894e+03<div class="im">
<br>
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.<br></div> 4.09985e+03 8.28955e+03 -1.68827e+04 -1.04035e+05 -1.38691e+05<br> Position Rest. Potential Kinetic En. Total Energy Temperature<br>
6.95754e+02 -2.24797e+05 0.00000e+00 -2.24797e+05 0.00000e+00<div class="im"><br> Pressure (bar)<br> 0.00000e+00<br><br></div>The position restraint is working fine as well....<br><br>Thank you so much.<br>
<br>Regards,