Hi, I am getting these notes when I run grompp:
NOTE 3 [file Init/ffsb_init.top]: 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. initialising group options... processing index file... Analysing residue names: There are: 3484 OTHER residues There are: 67 PROTEIN residues There are: 0 DNA residues There are: 0 RNA residues Analysing Protein... Analysing Other... Making dummy/rest group for Acceleration containing 11343 elements Making dummy/rest group for Freeze containing 11343 elements Making dummy/rest group for VCM containing 11343 elements Number of degrees of freedom in T-Coupling group Protein is 1777.76 Number of degrees of freedom in T-Coupling group non-Protein is 20898.23 Making dummy/rest group for User1 containing 11343 elements Making dummy/rest group for User2 containing 11343 elements Making dummy/rest group for XTC containing 10450 elements Making dummy/rest group for Or. Res. Fit containing 11343 elements Making dummy/rest group for QMMM containing 11343 elements T-Coupling has 2 element(s): Protein non-Protein Energy Mon. has 2 element(s): Protein non-Protein Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 2 element(s): Protein rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Largest charge group radii for Van der Waals: 0.288, 0.263 nm Largest charge group radii for Coulomb: 0.288, 0.263 nm NOTE 4 [file nvtp.mdp]: The sum of the two largest charge group radii (0.551009) is larger than rlist (2.000000) - rvdw (2.000000) Can someone tell me how to correct these? Pooja On Thu, Jul 15, 2010 at 7:06 PM, Sai Pooja <saipo...@gmail.com> wrote: > Hi, > > NOTE 4 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]: > The sum of the two largest charge group radii (0.510406) is larger than > rlist (2.000000) - rvdw (2.000000) > > > > NOTE 5 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]: > The sum of the two largest charge group radii (0.510406) is larger than > rlist (2.000000) - rcoulomb (1.800000) > > How does this effect the simulation? Do these introduce errors? > > Pooja > > -- > Quaerendo Invenietis-Seek and you shall discover. > -- Quaerendo Invenietis-Seek and you shall discover.
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