[gmx-users] Charge grps and cut-off

[Sai Pooja]

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.

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

Any thoughts?
Pooja



Pooja
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