[gmx-users] Charge grps and cut-off

[Justin A. Lemkul]

Sai Pooja wrote:
> 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?
> 

Note 3 is explained in detail in the error message.  Beyond that, read about the 
group concept in the manual.

I've never seen Note 4 before, but a 2-nm cutoff is a bit strange for a protein 
simulation.  Any reason you're using such large cutoffs?  You may also want to 
provide your whole .mdp file to see if anyone can spot the underlying issue.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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