I am trying to equilibrate a POPC membrane with 128 POPC molecules, but grompp gives out the following notes and minimization with mdrun does not work. The output on screen of mdrun comes out like this:<br>Steepest Descents converged to machine precision in 15 steps,<br>
but did not reach the requested Fmax < 10.<br>Potential Energy = 1.4422483e+17<br>Maximum force = inf on atom 4082<br>Norm of force = inf<br> <br>And grompp notes are:<br>NOTE 2 [file topol.top, line unknown]:<br>
The largest charge group contains 12 atoms.<br> Since atoms only see each other when the centers of geometry of the charge<br> groups they belong to are within the cut-off distance, too large charge<br> groups can lead to serious cut-off artifacts.<br>
For efficiency and accuracy, charge group should consist of a few atoms.<br> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br><br>NOTE 3 [file topol.top, line unknown]:<br> The largest charge group contains 16 atoms.<br>
Since atoms only see each other when the centers of geometry of the charge<br> groups they belong to are within the cut-off distance, too large charge<br> groups can lead to serious cut-off artifacts.<br> For efficiency and accuracy, charge group should consist of a few atoms.<br>
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br>Here is my minimization mdp file, I have used the first one with PME but then changed to Reaction-field and no PBC (just as curiosity to see if it worked).<br>
integrator = steep <br>emtol = 1000.0 <br>emstep = 0.01 <br>nsteps = 50000 <br>nstlist = 1 <br>ns_type = grid <br>rlist = 1.2 <br>coulombtype = PME <br>
rcoulomb = 1.2 <br>rvdw = 1.2 <br>pbc = xyz <br><br><br>Thank you<br>