[gmx-users] Charge distribution in the topology file

[James Starlight]

Dear Gromacs Users!


I want to perform in vacuum simulation for the simple peptid parametrised
by Amber 99SB and Gromos 43.1 force fields.


As I understoon the primary foal of in vacum simulation in the turn of all
charges in the residues wich are not exposed to the solvent.


>From topology file ( done by Amber) I've found such example for the Gly
residue as well for charged Glu

; residue 404 GLY rtp GLY  q  0.0
  6365          N    404    GLY      N   6365    -0.4157      14.01   ;
qtot -1.848
  6366          H    404    GLY      H   6366     0.2719      1.008   ;
qtot -1.576
  6367         CT    404    GLY     CA   6367    -0.0252      12.01   ;
qtot -1.601
  6368         H1    404    GLY    HA1   6368     0.0698      1.008   ;
qtot -1.531
  6369         H1    404    GLY    HA2   6369     0.0698      1.008   ;
qtot -1.461
  6370          C    404    GLY      C   6370     0.5973      12.01   ;
qtot -0.8642
  6371          O    404    GLY      O   6371    -0.5679         16   ;
qtot -1.432

; residue  28 GLU rtp GLU  q -1.0
   354          N     28    GLU      N    354    -0.5163      14.01   ;
qtot -2.516
   355          H     28    GLU      H    355     0.2936      1.008   ;
qtot -2.223
   356         CT     28    GLU     CA    356     0.0397      12.01   ;
qtot -2.183
   357         H1     28    GLU     HA    357     0.1105      1.008   ;
qtot -2.073
   358         CT     28    GLU     CB    358      0.056      12.01   ;
qtot -2.017
   359         HC     28    GLU    HB1    359    -0.0173      1.008   ;
qtot -2.034
   360         HC     28    GLU    HB2    360    -0.0173      1.008   ;
qtot -2.051
   361         CT     28    GLU     CG    361     0.0136      12.01   ;
qtot -2.038
   362         HC     28    GLU    HG1    362    -0.0425      1.008   ;
qtot -2.08
   363         HC     28    GLU    HG2    363    -0.0425      1.008   ;
qtot -2.123
   364          C     28    GLU     CD    364     0.8054      12.01   ;
qtot -1.317
   365         O2     28    GLU    OE1    365    -0.8188         16   ;
qtot -2.136
   366         O2     28    GLU    OE2    366    -0.8188         16   ;
qtot -2.955
   367          C     28    GLU      C    367     0.5366      12.01   ;
qtot -2.418
   368          O     28    GLU      O    368    -0.5819         16   ;
qtot -3

My qustions:

1- What is difference between charge value and charge B qtot value ?

2- Must I  turn off absolutely all charges even in the non-polar residues
e.g edit
-0.3662 value  to the 0.0000 for all atoms in Gly for instance. ? What
another edition should I do for the elimination of the charges ?

3- I've found that GROMOS force field is not good choise for the vacum
simulation because of non condensive phase of that system but in some works
authors use this ff for in vacum system. What should I do for the
adaptation of that ff for my system?


Thanks

James
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