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

[Faezeh Pousaneh]

Dear Justin,

How can I check that ''input configuration is "broken" across PBC'' ?
>From vmd it is hard to say, since I only have one component system.


Best regards


On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh <fpoosaneh at gmail.com>
wrote:

>
> 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=docume
>>> ntation#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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>
>