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

[David van der Spoel]

亀田倫史 wrote:
> 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?
> 
it is a system wide correction, but for water it is not relevant. 
therefore your conclusion is correct.

> 
> 
> Thanks.
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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