[gmx-users] Regarding the charge group radii

[rama david]

Hi ,

I am using G 96 53a6 ff with spc water model.
system has -32 charge...( ligand + protein...ligand is small peptide)
The charge on ligand is Zero
I am using the box of 13 nm dimension.

new system size : 10.583  7.915  6.259
    shift       :  1.932  1.122  7.068 (nm)
new center      :  6.500  6.500  6.500 (nm)
new box vectors : 13.000 13.000 13.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :2197.00               (nm^3)


I added water molecule by following command ....
genbox -cp princ.pdb  -cs spc216.gro -p topol.top  -o solvated.pdb


When I tried to neutralized the system,

grompp -f minim.mdp  -c  solvated.pdb  -o ion.tpr



I got the following error..





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


the mdp file I used


minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
define          = -DFLEXIBLE
integrator    = steep        ; Algorithm (steep = steepest descent
minimization)
emtol        = 1000.0      ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps        = 50000          ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist        = 1        ; Frequency to update the neighbor list and long
range forces
ns_type        = grid        ; Method to determine neighbor list (simple,
grid)
rlist           = 0.9        ; Cut-off for making neighbor list (short
range forces)
coulombtype    = PME        ; Treatment of long range electrostatic
interactions
rcoulomb    = 0.9         ; Short-range electrostatic cut-off
vdw-type        = Cut-off
rvdw        = 1.4        ; Short-range Van der Waals cut-off
pbc        = xyz         ; Periodic Boundary Conditions (yes/no)


I try without ligand.
The system has -32 charge.
I make the box of same dimension and mdp file

on
grompp -f minim.mdp  -c  solvated.pdb  -o ion.tpr
I got following out-put

Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 647877.00
Largest charge group radii for Van der Waals: 0.252, 0.252 nm
Largest charge group radii for Coulomb:       0.252, 0.252 nm
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




Please give me the suggestion to resolve the issue..!!



Thank you.
With Best Wishes and Regards,
Rama David.