[gmx-users] Protein-complex simulation

[Justin Lemkul]

On 1/6/17 1:58 AM, Nivedita Rai wrote:
> Dear gromacs User,
>                     I am running *protein ligand complex* simulation by
> following the Beven lab tutorial. while production run im getting two notes
> such as:
>
> NOTE 1 [file topol.top]:
>   The largest charge group contains 11 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.
>
> Number of degrees of freedom in T-Coupling group Protein_UNK is 8298.87
> Number of degrees of freedom in T-Coupling group Water_and_ions is 180606.12
> Largest charge group radii for Van der Waals: 0.267, 0.265 nm
> Largest charge group radii for Coulomb:       0.267, 0.265 nm
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 84x84x84, spacing 0.118 0.118 0.118
> Estimate for the relative computational load of the PME mesh part: 0.32
>
> NOTE 2 [file md.mdp]:
>   This run will generate roughly 5681 Mb of data
>
> Is *note1* will create any trouble? if yes then how to rectify it?
>

If you are using cutoff-scheme = Verlet, it is meaningless because charge groups 
are ignored (and this method is preferred).  If not, find that charge group and 
figure out if it is right because neighbor searching can be affected by charge 
groups that are too large.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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