[gmx-users] Warnings while grompp_d

[vivek sharma]

Hi there,
while running gromacs in parallel with double precision, during grompp_d I
am getting following warning in output file along with other status..


...
...
...
WARNING 1 [file 1XU9_A.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.
...
...
...
...
...
WARNING 2 [file aminoacids.dat, line 1]:
  T-Coupling group protein has fewer than 10% of the atoms (2626 out of
  45599)
  Maybe you want to try Protein and Non-Protein instead?
WARNING 3 [file aminoacids.dat, line 1]:
  T-Coupling group NDP has fewer than 10% of the atoms (61 out of 45599)
  Maybe you want to try Protein and Non-Protein instead?
......
.
.
.
.
.
What these warnings indicates and how can they be rectified ?

just a guess, Is there any relation with tau_t mentioned in .mdp file
corresponding to protein and NDP i.e. 0.1 (for warning 2 and 3)
if it is, then how can we reduce the number of sol atoms i.e. very high
43000(approx).

Any idea of this would be of great help.

With Thanks,
Vivek
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