[gmx-users] Charge grps and cut-off

[Justin A. Lemkul]

Sai Pooja wrote:
> A charge grp consisting of 12 atoms is created from Arginine residues in 
> my topology file. 
> 
> ; residue  14 ARG rtp ARG  q +1.0
>    476        NH1     14    ARG      N    150      -0.47     14.007   ; 
> qtot -3.47
>    477          H     14    ARG     HN    150       0.31      1.008   ; 
> qtot -3.16
>    478        CT1     14    ARG     CA    150       0.07     12.011   ; 
> qtot -3.09
>    479         HB     14    ARG     HA    150       0.09      1.008   ; 
> qtot -3    
>    480        CT2     14    ARG     CB    151      -0.18     12.011   ; 
> qtot -3.18 
>    481         HA     14    ARG    HB1    151       0.09      1.008   ; 
> qtot -3.09
>    482         HA     14    ARG    HB2    151       0.09      1.008   ; 
> qtot -3   
>    483        CT2     14    ARG     CG    152      -0.18     12.011   ; 
> qtot -3.18 
>    484         HA     14    ARG    HG1    152       0.09      1.008   ; 
> qtot -3.09 
>    485         HA     14    ARG    HG2    152       0.09      1.008   ; 
> qtot -3    
>    486        CT2     14    ARG     CD    153        0.2     12.011   ; 
> qtot -2.8  
>    487         HA     14    ARG    HD1    153       0.09      1.008   ; 
> qtot -2.71
>    488         HA     14    ARG    HD2    153       0.09      1.008   ; 
> qtot -2.62
>    489        NC2     14    ARG     NE    153       -0.7     14.007   ; 
> qtot -3.32
>    490         HC     14    ARG     HE    153       0.44      1.008   ; 
> qtot -2.88
>    491          C     14    ARG     CZ    153       0.64     12.011   ; 
> qtot -2.24
>    492        NC2     14    ARG    NH1    153       -0.8     14.007   ; 
> qtot -3.04
>    493         HC     14    ARG   HH11    153       0.46      1.008   ; 
> qtot -2.58
>    494         HC     14    ARG   HH12    153       0.46      1.008   ; 
> qtot -2.12
>    495        NC2     14    ARG    NH2    153       -0.8     14.007   ; 
> qtot -2.92
>    496         HC     14    ARG   HH21    153       0.46      1.008   ; 
> qtot -2.46
>    497         HC     14    ARG   HH22    153       0.46      1.008   ; 
> qtot -2   
>    498          C     14    ARG      C    154       0.51     12.011   ; 
> qtot -1.49
>    499          O     14    ARG      O    154      -0.51     15.999   ; 
> qtot -2   
> 
> See charge group 153. It has 12 atoms. This is true for all Arginine 
> residues. It seems that charge groups must have an integer net-charge. 
> As you can see, it assigns charge grps 151, 152, 153 etc. till the 
> net-charge becomes an integer.
>  

Strictly speaking, charge groups do not always have to have a net charge, but 
generally they do.

> One option would be to manually make them. In this case, I could simply 
> breakdown this particular charge grp into 2 smaller chargegrps but I am 
> sure if that would be consistent with the forcefield and not sure if it 
> would be possible to set the net charge to an integral value to an 
> integer for the smaller charge groups.

Simply breaking the charge group apart seems too arbitrary.  If you're not using 
PME (which you're not), then you need integral charge groups, so it looks like 
this one has to stay intact.  It just seems like there's the potential for 
inaccurate short-range interactions when the entire sidechain is encompassed by 
a single charge group.  Perhaps for your case it will not matter so much; maybe 
someone else can comment.  There are numerous threads in the list archive 
discussing this situation, so I won't repeat all of that here.

> Also, is there an alternate way by changing the Cut-off?
> 

Not really.  Any cutoff you choose might be affected by artifacts of a large 
charge group.

-Justin

> Any thoughts?
> Pooja
> 
> 
> 
> Pooja
> 

-- 
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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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