[gmx-users] Re: too much warnings and notes
Dr. Vitaly Chaban
vvchaban at gmail.com
Mon Oct 29 16:06:37 CET 2012
> NOTE 3 [file complex.top]:
> The largest charge group contains 12 atoms.
> Since atoms only see each other when the centers of geometry of the
> 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.
> Number of degrees of freedom in T-Coupling group Protein_LIG is 9475.34
> Number of degrees of freedom in T-Coupling group POPC is 33353.66
> Number of degrees of freedom in T-Coupling group Water_and_ions is 53973.00
> Largest charge group radii for Van der Waals: 0.299, 0.299 nm
> Largest charge group radii for Coulomb: 0.299, 0.299 nm
> NOTE 4 [file md.mdp]:
> The sum of the two largest charge group radii (0.597592) is larger than
> rlist (1.000000) - rvdw (1.200000)
The 3rd and 4th notes are expected to increase the instability of your
Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
More information about the gromacs.org_gmx-users