[gmx-users] Protein-Protein interaction using Generalized-Reaction-Field

[亀田倫史]

I'm going to confirm the protein-protein interaction energy.

If I carry out MD simulations with

coulombtype         =  Generalized-Reaction-Field
energygrps          =  Protein  OTHER

Then g_energy outputs

   1=          Bond   2=         Angle   3=   Proper Dih.   4=Ryckaert-Bell.
   5=         LJ-14   6=    Coulomb-14   7=       LJ (SR)   8=  Coulomb (SR)
   9=      RF excl.  10=     Potential  11=   Kinetic En.  12=  Total Energy
  13=   Temperature  14=Pressure (bar)  15=         Box-X  16=         Box-Y
  17=         Box-Z  18=        Volume  19=  Density (SI)  20=            pV
  21=        Vir-XX  22=        Vir-XY  23=        Vir-XZ  24=        Vir-YX
  25=        Vir-YY  26=        Vir-YZ  27=        Vir-ZX  28=        Vir-ZY
  29=        Vir-ZZ  30= Pres-XX (bar)  31= Pres-XY (bar)  32= Pres-XZ (bar)
  33= Pres-YX (bar)  34= Pres-YY (bar)  35= Pres-YZ (bar)  36= Pres-ZX (bar)
  37= Pres-ZY (bar)  38= Pres-ZZ (bar)  39= #Surf*SurfTen  40=  Pcoupl-Mu-XX
  41=  Pcoupl-Mu-YY  42=  Pcoupl-Mu-ZZ  43=          Mu-X  44=          Mu-Y
  45=          Mu-Z  46=Coul-SR:Protein-Protein  47=LJ-SR:Protein-Protein  48=Coul-14:Protein-Protein
  49=LJ-14:Protein-Protein  50=Coul-SR:Protein-Other  51=LJ-SR:Protein-Other  52=Coul-14:Protein-Other
  53=LJ-14:Protein-Other  54=Coul-SR:Other-Other  55=LJ-SR:Other-Other  56=Coul-14:Other-Other
  57=LJ-14:Other-Other  58=     T-Protein  59=       T-Other  60=  Lamb-Protein
  61=    Lamb-Other

I think numbers corresponding to protein-protein interaction energy are
9 46 47 48 49.

Especially, I'm interested in dealing with 9, 'RF excl.'.
Perhaps, this term means Reaction-field exclusion correction coded by Berk Hess,
(http://www.gromacs.org/features/changes33.html)
and affects 48, 'Coul-14:Protein-Protein'.

Is it correct?



Thanks.