Hello, I am trying to run a NVT equilibration of 2.5 ns of my protein-carbohydrate complex but its failing because I am getting this error message all the time
Step 33, time 0.033 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002814, max 0.053588 (between atoms 1553 and 1552) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1553 1552 90.0 0.1000 0.1054 0.1000 Step 34, time 0.034 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000318, max 0.005474 (between atoms 1553 and 1552) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1553 1552 70.0 0.1054 0.1005 0.1000 Step 35, time 0.035 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000320, max 0.005247 (between atoms 1553 and 1552) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1553 1552 79.9 0.1005 0.0995 0.1000 nvt.mdp title = 123 define = -DPOSRES -DPOSRES_LIGAND ; Run parameters integrator = md-vv ; leap-frog integrator nsteps = 2500000 ; 0.001 * 2500000 = 2500 ps dt = 0.001 ; 1 fs ; Output control nstxout = 5000 ; suppress .trr output nstvout = 5000 ; suppress .trr output nstenergy = 5000 ; save energies every 1000.0 ps nstlog = 5000 ; update log file every 1000.0 ps nstxtcout = 5000 xtc_precision = 100 energygrps = Protein LIG SOL ; 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 ns_type = grid ; search neighboring grid cells nstlist = 5 ; rcoulomb = 0.9 rvdw = 1.4 coulombtype = PME ; Particle Mesh Ewald for long- rlistlong = 1.4 rlist = 0.9 pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT periodic_molecules = yes ; Temperature coupling tcoupl = nose-hoover ; modified Berendsen thermostat tc-grps = Protein_LIG Water_and_ions ; two coupling groups - more accurate tau_t = 2.0 2.0 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; 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 Please help. -- Deep Bhattacharya. -- 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.
