[gmx-users] Fwd: protein-ligand complex simulation

Nivedita Rai bioinfonivedta at gmail.com
Fri Jan 13 12:44:04 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
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?

I have already posted this question twice. hope this time I will get the
Thanks and regards

Nivedita Rai
PhD in Bioinformatics

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