[gmx-users] CHarmm and popc membrane

[chris.neale at utoronto.ca]

I think the notes from grompp are pretty clear. You need to redivide  
your charge groups so that they contain fewer atoms. You can do this  
in the .top or .itp file and you can find out how to do that in the  
manual. Feel free to post your original and charge-group-modified  
topologies back here if you want people to take a look at them.

Chris.

-- original message --

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