[gmx-users] Regarding the charge group radii

[Justin Lemkul]

On 11/19/12 11:37 PM, rama david wrote:
> 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)
>

Apparently you have some giant charge groups.  If your system is a protein, 
peptide ligand, and water, all of your topologies should come from pdb2gmx and 
this should never happen.

>
> 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..!!
>

The second block of output suggests that the problem is with your peptide 
ligand.  Its removal gets rid of the problem, so it seems clear to me that its 
topology is incorrect.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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