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

[Faezeh Pousaneh]

Thanks Justin.
One component I mean system of only one type atom, each atom has two
charged virtual sites. So I can not see from VMD any breaking.


On Dec 17, 2017 8:10 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:



On 12/17/17 8:22 AM, Faezeh Pousaneh wrote:

> 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.
>

What is that one component? If a group of atoms is supposed to be in a
charge group, and it is split across the box, then you need to correct it
with trjconv or (if you are absolutely sure this isn't a problem) override
with grompp -maxwarn (dangerous and generally not wise).

-Justin



> 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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>>
-- 
==================================================

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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