[gmx-users] energy_extract

[Mark Abraham]

On 1/07/2011 4:40 PM, balaji nagarajan wrote:
> Dear Users !
>
> I have took a penta peptide and did topology generation ,
>
> I have solvated it with water box ,
>
> now i did a minimization with zero step , to know the energy of the 
> initial molecule ,
>
> i used g_energy for the out put ,
>
> like
>
> $ g_energy -f em.edr
>
> it gives as follows , i have to type number to get energy !
>
> --------------------------------------------------------------------
>
> but it lists 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.
> -------------------------------------------------------------------
>   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  T-rest
>
> ----------------------------
>
> Is there any way to get the energy of the protein and the energy of 
> protein and water alone

There is no way to decompose the existing contents of an .edr file. You 
need to use energy groups (see manual), either in your original 
simulation, or "after the fact" by using mdrun -rerun on your existing 
trajectory with a different .tpr.

Mark
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