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: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = 1.4422483e+17 Maximum force = inf on atom 4082 Norm of force = inf
And grompp notes are: NOTE 2 [file topol.top, line unknown]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. NOTE 3 [file topol.top, line unknown]: The largest charge group contains 16 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. 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). integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 50000 nstlist = 1 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 pbc = xyz Thank you
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