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

[Faezeh Pousaneh]

The sum of the two largest charge group radii (7.984601) is larger than
  rlist (0.347900).
the configuration looks fine across pbc. Everything looks normal. Following
is my md. I have user-specified potential so I need to have cut-off values
as given below.


integrator                = md
 dt                        = 0.001
 nsteps                    = 3000000
 nstxout                   = 100000           ; save coordinates every 0 ps
 nstvout                   = 100000           ; save velocities every 0 ps
 nstlog                    = 100000           ; update log file every
 nstenergy                 = 100000        ; save energies every
 nstxtcout                 = 100000       ; Output frequency for xtc file
 xtc-precision             = 100000       ; precision for xtc file
 ns_type                   = grid        ; search neighboring grid cells
 nstlist                   = 10           ;  fs
 pbc                       = xyz         ; 3-D PBC
 rlist                     = 0.3479      ; short-range neighborlist cutoff
(in nm)
 rcoulomb                  = 0.3479         ; short-range electrostatic
cutoff (in nm)
 rvdw = 0.3479; short-range van der Waals cutoff (in nm)
 coulombtype               = PME-user         ; Particle Mesh Ewald for
long-range electrostatics
 pme_order                 = 4           ; cubic interpolation
 fourierspacing            = 0.16        ; grid spacing for FFT
 vdw-type                  = user
 Tcoupl                    = berendsen   ; modified Berendsen thermostat
 tc-grps                   = co2   rest           ; two coupling groups -
more accurate
 tau_t                     =  0.1   0.1 ; time constant, in ps
 ref_t                     =  179.8  179.8 ; reference temperature, one for
each group, in K
 ;tc-grps                  = system
cutoff-scheme              =group
 energygrps                = co2 rest
 Pcoupl                    = no;Parrinello-Rahman
 Pcoupltype                = Isotropic
 tau_p                     = 1.0
 compressibility           = 6.2e-5
 ref_p                     = 50.0
 gen_vel                   = yes
 gen_temp                  = 179.8
 gen_seed                  = 712349
 DispCorr                  =no;  EnerPres    ; account for cut-off vdW
scheme
 constraints               = all-bonds   ; all bonds constrained (fixed
length)
 continuation              = no         ; Restarting after NPT
 constraint-algorithm      =  lincs       ; holonomic constraints
 lincs_iter                = 1           ; accuracy of LINCS
 lincs_order               = 4           ; also related to accuracy



Best regards


On Fri, Dec 15, 2017 at 1:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/15/17 4:26 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> I get this error only in NVT equlibration step, not in the NPT and
>> production steps. Should I worry about it?
>>
>> In gromacs page it tell the error can come from 4 reasons, but how I can
>> recognize which can be mine?
>>
>
> Check the size of your largest charge group, value of rlist, or whether or
> not the input configuration is "broken" across PBC.
>
> -Justin
>
> http://www.gromacs.org/Documentation/Errors?highlight=
>> documentation#The_sum_of_the_two_largest_charge_group_
>> radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
>>
>> Best regards
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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