[gmx-users] Protein-Protein interaction using Generalized-Reaction-Field
亀田倫史
kameda-tomoshi at aist.go.jp
Wed Mar 15 08:49:11 CET 2006
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.
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