[gmx-users] CHarmm and popc membrane

[Stefan Hoorman]

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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