Hi, I have installed 5.1.1, and am trying to run the simulations. During the run, I am getting this error as pasted below: WARNING: Listed nonbonded interaction between particles 1 and 9 at distance 9.500 which is larger than the table limit 2.030 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. Segmentation fault (core dumped) I have tried neutralizing the the charges, however, the error remains the same. I am using the NVT parameters as below: title = OPLS Lysozyme NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 10000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 1.0 ps nstvout = 1000 ; save velocities every 1.0 ps nstenergy = 1000 ; save energies every 1.0 ps nstlog = 1000 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; 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 When using on an older Gromacs version (older than 5.1), the run is smooth (everything else remaining constant). Can anyone help me to target the error? Whether it is due my hardware issue (its a dell inspiron with 4 GB RAM, i5 processor, 2 cores, 1.7 GHz) or I am making an error in the steps? Thanks, Kunal -- Dr. Kunal Maniar Resident, Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh (PGIMER) Mobile: +91 8968630447 Email id: drkunalman...@gmail.com -- 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.
