[gmx-users] CHarmm and popc membrane
Stefan Hoorman
stefhoor at gmail.com
Fri Jan 15 19:29:28 CET 2010
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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