[gmx-developers] energy group computation

[Berk Hess]

Hi,

This is a use, not a development question. Please post such questions to 
gmx-users.

But the quick answer is that although it's technically possible to 
calculate this number, this number is useless (and indeed high).

Cheers,

Berk

On 2015-08-27 19:00, ANTHONY C MANSON wrote:
> Hello:
>
> I am trying to estimate the polar solvation energy of a 76 residue
> protein at standard conditions.  I am using the gromacs 4.5.3 dp release.
> I have set up a simulation with the solvated  (using spce water) protein.
> I have defined two energygrps: Protein SOL in the *.mdp file.
> I have run the simulation and have then run g_energy on the *.edr file.
> I get the following choices from g_energy:
>
>   1  Bond       2  Angle            3  Proper-Dih.      4  Improper-Dih.
>   5  LJ-14      6  Coulomb-14       7  LJ-(SR)          8  Disper.-corr.
> 9  Coulomb-(SR)    10  Coul.-recip.    11  Potential       12 
>  Kinetic-En.
>  13  Total-Energy    14  Temperature     15  Pres.-DC        16  Pressure
>  17  Vir-XX        18  Vir-XY          19  Vir-XZ          20  Vir-YX
>  21  Vir-YY  22  Vir-YZ          23  Vir-ZX        24  Vir-ZY
>  25  Vir-ZZ          26  Pres-XX         27  Pres-XY   28  Pres-XZ
>  29  Pres-YX         30  Pres-YY   31  Pres-YZ         32  Pres-ZX
>  33  Pres-ZY   34  Pres-ZZ         35  #Surf*SurfTen   36  Mu-X
>  37  Mu-Y              38  Mu-Z
>  39  Coul-SR:Protein-Protein         40  LJ-SR:Protein-Protein
>  41  Coul-14:Protein-Protein             42  LJ-14:Protein-Protein
>  43  Coul-SR:Protein-SOL   44  LJ-SR:Protein-SOL
>  45  Coul-14:Protein-SOL             46  LJ-14:Protein-SOL
>  47  Coul-SR:SOL-SOL     48  LJ-SR:SOL-SOL
>  49  Coul-14:SOL-SOL                     50  LJ-14:SOL-SOL
>  51  T-System
>
> I pick Coul-SR:Protein-SOL as a component of the polar solvation energy.
> I note that the energy magnitude seems extremely high:
>
> Energy              Average   Err.Est.     RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Coul-SR:Protein-SOL        -8343.86         46    193.457  -192.93 
>  (kJ/mol)
>
> This seems unreasonable to me.  I wanted to understand how mdrun
> was calculating this value.  Perhaps it is accumulating energies over
> many frames.  What part of the code (force.c ...) handles this
> calculation so I can verify its action.
>
> Also, I tried running g_enemat on this with the following groups.dat file.
>
> 2
> Protein
> SOL
>
> I use the command:
>
> g_enemat  -f ub_short.edr -e 100
>
> and get:
>
> Opened ub_short.edr as double precision energy file
> Will read groupnames from in! putfile
> Read 2 groups
> group 0WARNING! could not find group (null):Protein-Protein (0,0)in 
> energy file
> WARNING! could not find group (null):Protein-SOL (0,1)in energy file
> group 1WARNING! could not find group (null):SOL-SOL (1,1)in energy file
>
> Will select half-matrix of energies with 6 elements
> Read frame: 1000, Time: 100.000e  100.000
> Will build energy half-matrix of 2 groups, 6 elements, over 1001 frames
> Segmentation fault
>
>
> Cheers
> Anthony Manson Ph.D.
>
>

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