[gmx-users] Re: Regarding the charge group radii

[Dr. Vitaly Chaban]

> When I tried to neutralized the system,
>
> grompp -f minim.mdp  -c  solvated.pdb  -o ion.tpr
>
>
>
> I got the following error..
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>
>
>
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> Analysing Protein...
> Number of degrees of freedom in T-Coupling group rest is 647865.00
> Largest charge group radii for Van der Waals: 4.108, 1.016 nm
> Largest charge group radii for Coulomb:       4.108, 1.072 nm
>
> WARNING 1 [file minim.mdp]:
>   The sum of the two largest charge group radii (5.180046) is larger than
>   rlist (0.900000)
>
>
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 112x112x112, spacing 0.116 0.116 0.116
> Estimate for the relative computational load of the PME mesh part: 0.37
>

I do not think that GROMPP is responsible for neutralizing the box.
Try an appropriate utility or add the ions by hand.


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark