Justin,Thanks for your reply. Then I wonder whether there is any other way out in gromacs to get the net interaction potential energy due to each of the components in a simulations. I am asking this, many times people report the potential energy contribution due to solvent-solvent interaction in a simulation containing solute( say peptide) and solvents and that are also being done in gromacs. I wonder, for those cases, whether just adding the non-bonding interaction will be good enough ? or, there is any other way out ?Jagannath
--- On Fri, 22/10/10, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] problem with energy groups and mdrun -rerun option To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Friday, 22 October, 2010, 2:56 AM jagannath mondal wrote: > 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-solvent > I get following output > > Here is the output from g_energy -f ener.edr : > > Select the terms you want from the following list by > selecting 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 ? Using energygrps only allows you to decompose nonbonded interactions. You cannot decompose bonded interactions, potential, kinetic energy, etc. -Justin > Any help will be useful. > Jagannath > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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