[gmx-users] Protein-ligand complex simulation
bioinfonivedta at gmail.com
Mon Jan 9 07:58:17 CET 2017
Dear Gromacs User,
I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
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?
Thanks and regards
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA
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