[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,
Graduate student-Chemical Engineering Department
Universidad de los Andes
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