This is my mdp file for energy minimization: constraints = none
; integration parameters integrator = l-bfgs dt = 0.00 nsteps = 15000 ; center of mass removal nstcomm = 10 comm_mode = Linear ; neighbour searching nstlist = 1 ns_type = grid pbc = xyz rlist = 1.4 ; electrostatics coulombtype = Reaction-Field-zero rcoulomb = 1.1 epsilon_r = 1.0 epsilon_rf = 0.0 ; van der Waals interactions vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ; Ewald parameters fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-6 optimize_fft = yes ; energy minimization emtol = 0.1 emstep = 0.01 And this is the one for MD constraints = none ; integration parameters integrator = md tinit = 0 dt = 0.001 nsteps = 10000000 ;init_step = 0 comm_mode = linear nstcomm = 10 ; output control nstxout = 10000 nstvout = 10000 nstfout = 0 nstlog = 10000 energygrps = hexane-UA ethanol ; neigbour searching nstlist = 1 ns_type = grid pbc = xyz rlist = 1.4 ; electrostatics coulombtype = Reaction-Field-zero rcoulomb = 1.1 epsilon_r = 1.0 epsilon_rf = 0.0 ; van der Waals interactions vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ; Ewald parameters fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-6 optimize_fft = yes ; Generate velocities gen_vel = yes gen_temp = 298.0 gen_seed = -1 To use as the starting configuration the last configuration of the minimization, I used the confout.gro file of the minimization as the input conf.gro for MD. I also tried using the traj.trr file generated after minimization with the grompp option -t for MD. I used the same top and ndx files in both simulations. Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/Potential-energy-from-a-previous-configuration-mismatch-tp5003352p5003359.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
