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