Hi all, I am trying to simulate a protein using similar parameters as in the tutorial - Protein ligand by Justin Lemkul.
I am facing a problem wherein the protein simulation is exploding only in this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4. The warning message is as follows ------------------------------------------------------- There were 4 inconsistent shifts. Check your topology Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 WARNING: Listed nonbonded interaction between particles 1312 and 1315 at distance 4.728 which is larger than the table limit 2.000 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. -------------------------------------------------------- ATOM 1312 O TYR A 207 ATOM 1315 CD1 TYR A 207 --------------------------------------------------------- ------------------------------------------------------------------- em_real.mdp file ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions ------------------------------------------------------------------------ The initial minimization step itself fails. I have tried to simulate a minimized structure as well, I still encounter the same problem. I would appreciate any help in this regard. I would also like to know if this means, that the results from the older version of gromacs reliable? Thanking you in anticipation Nisha -- 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.