[gmx-users] ARG Charmm gmx 4.5.1

[Baofu Qiao]

You  should change the charge group number. Every charge group include
several, like 3-4, atoms. Actually, the definition of charge group is
not significant if you use PME for the coulomb interaction.


nahren manuel wrote:
> Dear Gromacs Users,
>
> I am using plain cutoff for my 12-mer protein.
> The grompp reports ARG to have a big charge group. this was also highlighted in the following mail
> http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html
>
> I was just think if changing the charges on these atoms would help,
> from
> 13    CT2      1    ARG     CD     4        0.2     12.011   ; qtot 1.2
> 14     HA      1    ARG    HD1     4       0.09      1.008   ; qtot 1.29
> 15     HA      1    ARG    HD2     4       0.09      1.008   ; qtot 1.38
> 16    NC2      1    ARG     NE     4       -0.7     14.007   ; qtot 0.68
> 17     HC      1    ARG     HE     4       0.44      1.008   ; qtot 1.12
> 18      C      1    ARG     CZ     4       0.64     12.011   ; qtot 1.76
> 19    NC2      1    ARG    NH1     4       -0.8     14.007   ; qtot 0.96
> 20     HC      1    ARG   HH11     4       0.46      1.008   ; qtot 1.42
> 21     HC      1    ARG   HH12     4       0.46      1.008   ; qtot 1.88
> 22    NC2      1    ARG    NH2     4       -0.8     14.007   ; qtot 1.08
> 23     HC      1    ARG   HH21     4       0.46      1.008   ; qtot 1.54
> 24     HC      1    ARG   HH22     4       0.46      1.008   ; qtot 2
>
>
>
> to
>
>
>
>
> 	
> 	
> 	
> 	
> 	
> 		
>    CD    0.18
>   HD1    0.06
>   HD2    0.06
>    NE    -0.7
>    HE    0.4
>    CZ    0.6
>   NH1    -0.8
>  HH11    0.5
>  HH12    0.5
>   NH2    -0.8
>  HH21    0.5
>  HH22    0.5
>
> The above transformation of charges seems reasonable.
>
> Would like to know if this is okay...
>
>
> Best,
> nahren
>
>
>
>
>
>       
>