[gmx-users] Charge grps and cut-off

[Sai Pooja]

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 <saipooja at 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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