Hello, I have simulated a system of DNA and Protamine (Coarse grained, Martini). I want to look at the interaction energy between different groups like DNA - Protamine, DNA - ions, etc. I have defined energy groups in the mdp file, and I pass the index file with the groups while building the tpr file. After the run is complete, when I run gmx energy command, no matter what interaction energy I choose, it always gives me 0 (for all time steps). But the total Potential energy works. I am not able to understand why?
This is how my .mdp file looks like : title = NVT equilibration with position restraint on all solute (topology modified) ; Run parameters integrator = md ; leap-frog integrator nsteps = 60000000 ; 1 * 500000 = 500 ps ;nsteps = 5000 dt = 0.01 ; 1 fs ; Output control nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save velocities every 10 ps nstcalcenergy = 50 nstenergy = 1000 ; save energies every 1 ps nstxtcout = 2500 ;nstxout-compressed = 5000 ; save compressed coordinates every 1.0 ps ; nstxout-compressed replaces nstxtcout ;compressed-x-grps = System ; replaces xtc-grps nstlog = 1000 ; update log file every 1 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained ;lincs_iter = 2 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy epsilon_r = 15 ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cels nstlist = 10 ; 20 fs rvdw_switch = 1.0 rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = Cut-off ; Twin range cut-offs rvdw >= rlist ;vdw-modifier = Force-switch ;Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = v-rescale tc_grps = System tau_t = 1.0 ref_t = 300 energygrps = DNA Protein W ION freezegrps = DNA freezedim = Y Y Y ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correctiion DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 50 comm-mode = Linear comm-grps = System ; refcoord_scaling = com I would greatly appreciate any help. Thanks in advance, Thanks and Regards, Arnab Mukherjee -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.