[gmx-users] sum of the two largest charge group radii is larger than rlist

[abhisek Mondal]

I converted nvt.trr into .pdb file using following command:
*trjconv_mpi -f nvt.trr -o complex.pdb -s nvt.tpr -n index.ndx* and used
Protein_ACO as output group. Manual inspection in vmd shows ligand and
protein is perfectly paired and well inside the pbc box. Then why is
the *grompp_mpi
-f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr* command
is generating such error ? Please help me out here regarding the issue.

Thanks


On Wed, Mar 22, 2017 at 12:10 PM, abhisek Mondal <abhisek.mndl at gmail.com>
wrote:

> Hi,
>
>    I was trying to perform a NPT equilibration (after a NVT equilibration
> of 20ns) on a Protein-Ligand system when I got this error. I have protein,
> my ligand (ACO) and solvents in my system. I have tried to link the ligand
> to the protein using index.ndx file. However, I could not understand what
> is going wrong or my system is blowing up.
>
> When I pass *grompp_mpi -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n
> index.ndx -o npt.tpr* command, I'm getting *The sum of the two largest
> charge group radii (37.622505) is larger than rlist (1.400000)*.
>
>
> The NPT code I'm using is:
> title       = NPT Equilibration
> define      = -DPOSRES -DPOSRES_LIG    ; position restrain the protein and
> ligand
> ; Run parameters
> integrator  = md                ; leap-frog integrator
> nsteps      = 10000000          ; 2 * 10000000 = 20000 ps
> dt          = 0.002             ; 2 fs
> ; Output control
> nstxout     = 1000              ; save coordinates every 2 ps
> nstvout     = 1000              ; save velocities every 2 ps
> nstenergy   = 1000              ; save energies every 2 ps
> nstlog      = 1000              ; update log file every 2 ps
> ; Bond parameters
> continuation         = yes        ; Initial simulation
> constraint_algorithm = lincs     ; holonomic constraints
> constraints          = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter           = 1         ; accuracy of LINCS
> lincs_order          = 4         ; also related to accuracy
> ; Neighborsearching
> ns_type     = grid              ; search neighboring grid cels
> nstlist     = 5                 ; 10 fs
> rlist       = 1.4               ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.4               ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.4               ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order = 4             ; cubic interpolation
> fourierspacing  = 0.12          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl      = V-rescale             ; Berendsen is not suitable for
>  free-energy calculations, so using this
> tc-grps     = Protein_ACO  Water_and_ions ; two coupling groups - more
> accurate
> tau_t       = 0.1 0.1         ; time constant, in ps
> ref_t       = 310 310         ; reference temperature, one for each
> group, in K
> ; Pressure coupling is on
> pcoupl              = Berendsen     ; Pressure coupling on in NPT, also
> weak coupling
> pcoupltype          = isotropic     ; uniform scaling of x-y-z box vectors
> tau_p               = 2.0           ; time constant, in ps
> ref_p               = 1.0           ; reference pressure (in bar)
> compressibility     = 4.5e-5        ; isothermal compressibility, bar^-1
> refcoord_scaling    = com
> ; Periodic boundary conditions
> pbc     = xyz                   ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres          ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = no               ; Velocity generation is off, as continuing
> from NVT
> gen_temp    = 310               ; temperature for velocity generation
> gen_seed    = -1                ; random seed
> ; COM motion removal
> ; These options remove COM motion of the system
> nstcomm         = 10
> comm-mode       = Linear
> comm-grps       = System
>
>
> Please suggest me necessary modifications, if necessary, to complete NPT
> equilibration successfully.
>
> Thank you.
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*