Dear Gromacs users, Good someone give me a hit about the following issue. I am running a system which contains few periodic molecules (graphene sheets). Everything was running fine when the simulations were performed using group cut-off scheme and GROMACS 4.5.7. However, when I tried to transfer the same system to 5.0.4 version and switch from group to Verlet scheme the run crashed with the following error: "There were 80 inconsistent shifts. Check your topology"
No changes in topology files were performed. The difference in MDP files between two cases is shown below. Am I doing something obviously wrong? Many thanks in advance, Mikhail MDP-file for 5.0.4 (error about inconsistent shifts ) pbc = xyz ; periodic boundary conditions cutoff-scheme = Verlet verlet-buffer-drift = 0.005 ;================== Electrostatics coulombtype = PME rcoulomb = 1.2 ; cut-off for coulomb ;================== Van der Waals vdw-type = switch rvdw_switch = 1.0 rvdw = 1.2 ; cut-off for vdw ;================== EWALD/PME/PPPM parameters fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = yes ; perform FFT optimization at start old MDP-file for 4.5.7 (running without any trouble) pbc = xyz ; periodic boundary conditions periodic-molecules = yes ; in the system present periodic molecules rlist = 1.5 ; cut-off for ns ;================== Electrostatics coulombtype = PME rcoulomb = 1.5 ; cut-off for coulomb ;================== Van der Waals vdw-type = switch rvdw_switch = 1.0 rvdw = 1.2 ; cut-off for vdw ;================== EWALD/PME/PPPM parameters fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = yes ; perform FFT optimization at start -- 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.
