I am trying to rerun a simulation using this command mdrun -rerun -v -deffnm md
I think I must have made a mistake when I prepared the original mdp file because I get this message Number of atoms in trajectory (3883) does not match the run input file (37770) I have these files in my directory Complex.top ener.edr job.xml md.cpt md.edr md.gro md.log md.mdp md_prev.cpt md.tpr md.trr md.xtc traj.trr Here is my mdp file, should I remove entries for xtc_grps and energygrps to avoid this issue? integrator = md nsteps = 50000 dt = 0.002 nstvout = 5000 nstlog = 500 nstenergy = 250 nstxtcout = 5000 nstxout = 5000 xtc_grps = Protein LIG energygrps = Protein SOL constraints = all-bonds nstcomm = 1 ns_type = grid rlist = 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 Pcoupl = parrinello-rahman PcOupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes gen_seed = 805087 -- 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/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/mailing_lists/users.php
