[gmx-users] interaction energy

[Justin A. Lemkul]

balaji nagarajan wrote:
> Dear Users !
> 
> Now i am able to do the protein solvent interaction !
> 
> thanks ! i have understood !
> 
> when i used the energygrps  ,
> when i used the
> g_energy -f em.edr
> 
> this command it prints all terms and asks to make selection as below,
> 
>  1  Bond             2  Angle            3  Proper-Dih.      4  
> Ryckaert-Bell.
>   5  LJ-14            6  Coulomb-14       7  LJ-(SR)          8  LJ-(LR)
>   9  Coulomb-(SR)    10  Coul.-recip.    11  Potential       12  Pressure
>  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         23  Pres-XY         24  Pres-XZ
>  25  Pres-YX         26  Pres-YY         27  Pres-YZ         28  Pres-ZX
>  29  Pres-ZY         30  Pres-ZZ         31  #Surf*SurfTen   32  Mu-X
>  33  Mu-Y                                34  Mu-Z
>  35  Coul-SR:Protein-Protein             36  LJ-SR:Protein-Protein
>  37  LJ-LR:Protein-Protein               38  Coul-14:Protein-Protein
>  39  LJ-14:Protein-Protein               40  Coul-SR:Protein-SOL
>  41  LJ-SR:Protein-SOL                   42  LJ-LR:Protein-SOL
>  43  Coul-14:Protein-SOL                 44  LJ-14:Protein-SOL
>  45  Coul-SR:SOL-SOL                     46  LJ-SR:SOL-SOL
>  47  LJ-LR:SOL-SOL                       48  Coul-14:SOL-SOL
>  49  LJ-14:SOL-SOL   50  T-rest
> 
> -------------------------------------------------------
> 
> how one can write this all to a file !
> 

As prompted by g_energy:

"Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero."

Writing all terms to the same output file will result in nothing but an 
incoherent mess.  Choose terms wisely based on what you actually need to analyze.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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