[gmx-users] A note while running grompp for nvt equilibration

[Anu Chandran]

Dear users,
I am tyring to do a simulation of a monomer and an octamer of the same
molecule
using gromacs 4.5.3 with opls force field. Monomer simulations ran with out
any note or
warning, but when i tried to do nvt equilibration for the octamer, i got the
following note while running grompp

"NOTE 1 [file nvt.mdp]:
  The sum of the two largest charge group radii (0.779095) is larger than
  rlist (1.400000) - rvdw (1.000000)"
The mdp file used is as follows:

define                  = -DPOSRES
integrator              = md
dt                      = 0.002
nsteps                  = 50000
nstcomm                 = 10
nstxout                 = 100
nstvout                 = 100
nstlog                  = 100
nstenergy               = 100
nstlist                 = 5
ns_type                 = grid
pbc                     = xyz
rlist                   = 1.4
coulombtype             = PME
rcoulomb                = 1.4
epsilon_r               = 1
vdwtype                 = Switch
rvdw_switch             = 0.9
rvdw                    = 1.00
fourierspacing          = 0.12
pme_order               = 4
ewald_rtol              = 1e-5
optimize_fft            = yes
Tcoupl                  = nose_hoover
tc_grps                 = Protein  Non-Protein
tau_t                   = 0.4      0.4
ref_t                   = 300      300
nh-chain-length         = 1
pcoupl                  = no
gen_vel                 = yes
gen_temp                = 300.0
gen_seed                = 1984
continuation             = no
constraints              = all-bonds
constraint-algorithm     = LINCS
lincs-order              = 4
lincs-iter               = 1
lincs-warnangle          = 30


Can anybody please help me on how to go about with it?


Thank you,

with regards
Anu