<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi,<div> I have used gromacs 4.0.7 to do MD simulation of two solutes A & B in water ( solvent) . </div><div>Initially, I had set "energy groups = system " and used mdrun to do the simulation.</div><div><br></div><div>Now,I wanted to get the potential energy contribution from due to interaction of A-A, B-B,A-B A-solvent, B-solvent, solvent-solvent.</div><div>For that I followed some discussions in mailing list regarding using mdrun -rerun option:</div><div>This is what I did:</div><div>I used make_ndx and created 3 groups: A, B and solvent. </div><div>Now, I modified the grompp.mdp file so that I have now </div><div> energy groups = A B solvent </div><div><br></div><div>Then I used grompp -c conf -f grompp -n index -o topol</div><div><br></div><div>Then I used mdrun -s -rerun
traj_old.xtc </div><div><br></div><div>( here traj_old.xtc is the old xtc file I obtained during the original mdrun)</div><div><br></div><div>But, now, after using this -rerun option , if I try to use the g_energy on the resulting ener.edr file to obtain the individual potential energy of interaction for A-A, B-B , A-B, A-solvent</div><div>I get following output </div><div><br></div><div><br></div><div>Here is the output from g_energy -f ener.edr :</div><div><br></div><div><div>Select the terms you want from the following list by</div><div>selecting either (part of) the name or the number or a combination.</div><div>End your selection with an empty line or a zero.</div><div>-------------------------------------------------------------------</div><div> 1 Bond 2 Angle 3 U-B 4
Ryckaert-Bell.</div><div> 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) </div><div> 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Kinetic-En. </div><div> 13 Total-Energy 14 Conserved-En. 15 Temperature 16 Pressure-(bar)</div><div> 17 Cons.-rmsd-() 18 Vir-XX 19 Vir-XY 20 Vir-XZ </div><div> 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX </div><div> 25 Vir-ZY
26 Vir-ZZ 27 Pres-XX-(bar) 28 Pres-XY-(bar) </div><div> 29 Pres-XZ-(bar) 30 Pres-YX-(bar) 31 Pres-YY-(bar) 32 Pres-YZ-(bar) </div><div> 33 Pres-ZX-(bar) 34 Pres-ZY-(bar) 35 Pres-ZZ-(bar) 36 #Surf*SurfTen </div><div> 37 Mu-X 38 Mu-Y 39 Mu-Z 40 Coul-SR:A-A </div><div> 41 LJ-SR:A-A 42 Coul-14:A-A 43 LJ-14:A-A 44 Coul-SR:A-B </div><div> 45 LJ-SR:A-B 46 Coul-14:A-B
</div><div> 47 LJ-14:A-B 48 Coul-SR:A-Solvent </div><div> 49 LJ-SR:A-Solvent 50 Coul-14:A-Solvent </div><div> 51 LJ-14:A-Solvent 52 Coul-SR:B-B </div><div> 53 LJ-SR:B-B 54 Coul-14:B-B </div><div> 55 LJ-14:B-B
56 Coul-SR:B-Solvent </div><div> 57 LJ-SR:B-Solvent 58 Coul-14:B-Solvent </div><div> 59 LJ-14:B-Solvent 60 Coul-SR:Solvent-Solvent </div><div> 61 LJ-SR:Solvent-Solvent 62 Coul-14:Solvent-Solvent </div><div> 63 LJ-14:Solvent-Solvent 64 T-System </div><div> 65
Xi-System</div></div><div><br></div><div><div>It provides me contribution from each of the energy groups on nonbonding terms: LJ(SR),Coulomb(SR),Coulomb(14),LJ(14) . But, it does NOT provide me their contribution to Bonding term( i.e bond,angle, U-B,RB,improper-Dih) !! </div><div>As a result, I am a not sure how to get the net potential energy from each of the 3 energy groups. Am I doing something wrong ? Do I need to use any other utilities ?</div><div> Any help will be useful. </div></div><div><br></div><div>Jagannath</div><div><br></div></td></tr></table><br>