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<div class="moz-cite-prefix">Hi,<br>
<br>
This is a use, not a development question. Please post such
questions to gmx-users.<br>
<br>
But the quick answer is that although it's technically possible to
calculate this number, this number is useless (and indeed high).<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2015-08-27 19:00, ANTHONY C MANSON wrote:<br>
</div>
<blockquote cite="mid:1440694855l.7209130l.0l@psu.edu" type="cite">
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<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>
<br>
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