[gmx-developers] energy group computation

ANTHONY C MANSON acm20 at psu.edu
Thu Aug 27 19:50:29 CEST 2015

I am trying to estimate the polar solvation energy of a 76 residueprotein 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 overmany frames.  What part of the code (force.c ...) handles thiscalculation so I can verify its action.
Also, I tried running g_enemat on this with the following groups.dat file.
I use the command:
g_enemat  -f ub_short.edr -e 100
and get:
Opened ub_short.edr as double precision energy fileWill read groupnames from inputfileRead 2 groupsgroup 0WARNING! could not find group (null):Protein-Protein (0,0)in energy fileWARNING! could not find group (null):Protein-SOL (0,1)in energy filegroup 1WARNING! could not find group (null):SOL-SOL (1,1)in energy file
Will select half-matrix of energies with 6 elementsRead frame: 1000, Time: 100.000e  100.000         Will build energy half-matrix of 2 groups, 6 elements, over 1001 framesSegmentation fault

CheersAnthony Manson Ph.D.

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