Hi, I have used gromacs 4.0.7 to do MD simulation of two solutes A & B in water ( solvent) . Initially, I had set "energy groups = system " and used mdrun to do the simulation. 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.For that I followed some discussions in mailing list regarding using mdrun -rerun option:This is what I did:I used make_ndx and created 3 groups: A, B and solvent. Now, I modified the grompp.mdp file so that I have now energy groups = A B solvent Then I used grompp -c conf -f grompp -n index -o topol Then I used mdrun -s -rerun traj_old.xtc ( here traj_old.xtc is the old xtc file I obtained during the original mdrun) 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-solventI get following output
Here is the output from g_energy -f ener.edr : Select the terms you want from the following list byselecting either (part of) the name or the number or a combination.End your selection with an empty line or a zero.------------------------------------------------------------------- 1 Bond 2 Angle 3 U-B 4 Ryckaert-Bell. 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Kinetic-En. 13 Total-Energy 14 Conserved-En. 15 Temperature 16 Pressure-(bar) 17 Cons.-rmsd-() 18 Vir-XX 19 Vir-XY 20 Vir-XZ 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX-(bar) 28 Pres-XY-(bar) 29 Pres-XZ-(bar) 30 Pres-YX-(bar) 31 Pres-YY-(bar) 32 Pres-YZ-(bar) 33 Pres-ZX-(bar) 34 Pres-ZY-(bar) 35 Pres-ZZ-(bar) 36 #Surf*SurfTen 37 Mu-X 38 Mu-Y 39 Mu-Z 40 Coul-SR:A-A 41 LJ-SR:A-A 42 Coul-14:A-A 43 LJ-14:A-A 44 Coul-SR:A-B 45 LJ-SR:A-B 46 Coul-14:A-B 47 LJ-14:A-B 48 Coul-SR:A-Solvent 49 LJ-SR:A-Solvent 50 Coul-14:A-Solvent 51 LJ-14:A-Solvent 52 Coul-SR:B-B 53 LJ-SR:B-B 54 Coul-14:B-B 55 LJ-14:B-B 56 Coul-SR:B-Solvent 57 LJ-SR:B-Solvent 58 Coul-14:B-Solvent 59 LJ-14:B-Solvent 60 Coul-SR:Solvent-Solvent 61 LJ-SR:Solvent-Solvent 62 Coul-14:Solvent-Solvent 63 LJ-14:Solvent-Solvent 64 T-System 65 Xi-System 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) !! 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 ? Any help will be useful. Jagannath
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