Thank you for your Help. I did the following tc-groups
tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = extra34 Non-Protein energy ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 310 310 310 ; reference temperature, one for each group, in K ; Energy contain the residues that i needed extra34 contain all the remaining ligand and receptor atom non-protein contain sol and ion. I got the energy file after mdrun -rerun I used the g_energy term It give me the following output End your selection with an empty line or a zero. ------------------------------------------------------------------- 1 G96Angle 2 Proper-Dih. 3 Improper-Dih. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Kinetic-En. 13 Total-Energy 14 Temperature 15 Pres.-DC 16 Pressure 17 Constr.-rmsd 18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X 48 Mu-Y 49 Mu-Z 50 T-extra34 51 T-non-Protein 52 T-energy 53 Lamb-extra34 54 Lamb-non-Protein 55 Lamb-energy So I confused. though it shows the energy group, which option should i have to choose ?? What is Lamb-energy??? Is I did any mistake??? or I have to use any else command ?? Thank you in advance With best wishes and regards. Rama david. On Fri, Oct 5, 2012 at 7:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/5/12 10:16 AM, rama david wrote: > >> Hi gromacs friends, >> >> I completed the simulation of receptor and ligand, >> I visualized the trajectory in the vmd I found most of the time C >> terminal >> (ARG) interact with receptor ( 320 ASP) . >> I want to find out these interaction energy between these two residues in >> the simulation. >> >> >> >> How to find these interaction energy???? >> >> ( include the LJ and electrostatic interaction).. >> >> > I explained how to do this already. You need properly set energygrps in > the .mdp file and an index file that specifies those groups. The > quantities you want will then be in the .edr file like all other energy > terms. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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