[gmx-users] renumber charge group

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear user,
> 
> Please see attached file. I renumbered the "cgnr" of a ligand. Is there 
> any mistake related to renumbered of "cgnr"?

I see nothing unreasonable.

> 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

The error simply means you have atoms flying across your unit cell, thus it is 
blowing up.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

> [ 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 
> <tel:2%C2%A0%C2%A0%C2%A0%200.463%C2%A0%C2%A0%201.0080>
>     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 
> <tel:3%C2%A0%C2%A0%C2%A0%200.463%C2%A0%C2%A0%201.0080>
>    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 
> <tel:4%C2%A0%C2%A0%C2%A0%200.463%C2%A0%C2%A0%201.0080>      ;  1.000
> ; total charge of the molecule:   1.000
> 
> -- 
> Ahmet Yıldırım
> 
> 
> ------------------------------------------------------------------------
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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