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

[abhisek Mondal]

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*