[gmx-users] potential energy for solute only (g_energy)

[David van der Spoel]

On Sun, 2003-03-16 at 22:59, Lukas wrote:
> Hi all,
> 
> I already figured out, that one needs to define e. g.
> energygrps          =  PROTEIN   SOL
> in the input .mdp file.
> After the mdrun I analyse the .edr file with g_energy.
> 
> Now i have troubles to get the meaning of all those parts.
> 
>    1=      G96Angle   2=   Proper Dih.   3= Improper Dih.   4=         LJ-14
>    5=    Coulomb-14   6=       LJ (SR)   7=  Coulomb (SR)   8=     Potential
>    9=   Kinetic En.  10=  Total Energy  11=   Temperature  12=Pressure (bar)
>   13=        Vir-XX  14=        Vir-XY  15=        Vir-XZ  16=        Vir-YX
>   17=        Vir-YY  18=        Vir-YZ  19=        Vir-ZX  20=        Vir-ZY
>   21=        Vir-ZZ  22= Pres-XX (bar)  23= Pres-XY (bar)  24= Pres-XZ (bar)
>   25= Pres-YX (bar)  26= Pres-YY (bar)  27= Pres-YZ (bar)  28= Pres-ZX (bar)
>   29= Pres-ZY (bar)  30= Pres-ZZ (bar)  31= #Surf*SurfTen  32=          Mu-X
>   33=          Mu-Y  34=          Mu-Z  35=Coul-SR:Protein-Protein  36=LJ:Protein-Protein
>   37=Coul-14:Protein-Protein  38=LJ-14:Protein-Protein  39=Coul-SR:Protein-SOL  40=LJ:Protein-SOL
>   41=Coul-14:Protein-SOL  42=LJ-14:Protein-SOL  43=Coul-SR:Protein-rest  44=LJ:Protein-rest
>   45=Coul-14:Protein-rest  46=LJ-14:Protein-rest  47=Coul-SR:SOL-SOL  48=    LJ:SOL-SOL
>   49=Coul-14:SOL-SOL  50= LJ-14:SOL-SOL  51=Coul-SR:SOL-rest  52=   LJ:SOL-rest
>   53=Coul-14:SOL-rest  54=LJ-14:SOL-rest  55=Coul-SR:rest-rest  56=  LJ:rest-rest
>   57=Coul-14:rest-rest  58=LJ-14:rest-rest  59=     T-Protein  60=  Lamb-Protein
>   61=         T-SOL  62=      Lamb-SOL  63=          T-FE  64=       Lamb-FE
> 
> 
> which parts do i have to add to get the total potential energy of the protein, without the interactions with the solvent?
> 
> maybe
> 35=Coul-SR:Protein-Protein,
> 36=LJ:Protein-Protein,
> 37=Coul-14:Protein-Protein
> 38=LJ-14:Protein-Protein
> 
> How can I add the bonded terms? what is rest and lamb? (rest maybe restraint)
1 2 3 4 5 

rest is anything not explicitly defined (ions?)
lamb is the temperature coupling scaling factor
> 
> Thanks a lot in advance. Cheers,
> 
> Lukas
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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://xray.bmc.uu.se/~spoel
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