[gmx-users] Notes and warnings using grompp

Sonia Milena Aguilera Segura sm.aguilera37 at uniandes.edu.co
Fri Sep 28 22:32:49 CEST 2012


I´m getting the following notes when using grompp to generate the tpr file. My system is a protein in water. I already checked the topology file and the sum of my charges are -13. Should I ignore it? Why is it assuming that value?

NOTE 1 [file OmpC.top, line 23461]:
  System has non-zero total charge: -13.000002
  Total charge should normally be an integer.

The second note is the following.

Largest charge group radii for Van der Waals: 0.250, 0.244 nm
Largest charge group radii for Coulomb:       0.084, 0.084 nm

NOTE 2 [file min0.0.mdp]:
  The sum of the two largest charge group radii (0.494582) is larger than
  rlist (1.000000) - rvdw (0.900000)

Thank you in advance,

Sonia Aguilera
Graduate student-Chemical Engineering Department
Universidad de los Andes

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