[gmx-users] renumber charge group

[ahmet yıldırım]

Dear user,

Please see attached file. I renumbered the "cgnr" of a ligand. Is there any
mistake related to renumbered of "cgnr"?
I get the following error when I run position restrain (pr.mdp)

mdrun -deffnm pr
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
[ moleculetype ]
; Name   nrexcl
TRIS     3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1   CH0    1    TRIS      C    1    0.143  12.0110
    2    NL    1    TRIS      N    1   -0.590  14.0067
    3     H    1    TRIS      H    1    0.399   1.0080
    4     H    1    TRIS      H    1    0.399   1.0080
    5     H    1    TRIS      H    1    0.399   1.0080
    6   CH2    1    TRIS      C    2    0.257  14.0270
    7    OA    1    TRIS      O    2   -0.637  15.9994
    8     H    1    TRIS      H    2    0.463   1.0080
    9   CH2    1    TRIS      C    3    0.257  14.0270
   10    OA    1    TRIS      O    3   -0.637  15.9994
   11     H    1    TRIS      H    3    0.463   1.0080
   12   CH2    1    TRIS      C    4    0.257  14.0270
   13    OA    1    TRIS      O    4   -0.636  15.9994
   14     H    1    TRIS      H    4    0.463   1.0080      ;  1.000
; total charge of the molecule:   1.000

-- 
Ahmet Yıldırım
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