Dear Gmx Users, I am running REMD of a small protein in water. I have 36 temperatures. After minimization I equilibrate each with nvt and npt ensemble. Then I start REMD with -multidir. The mdp:
; Run parameters integrator = md ; leap-frog integrator nsteps = 50000000 dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 0.2 ps nstvout = 0 ; save velocities every 0.2 ps nstenergy = 5000 ; save energies every 0.2 ps nstxtcout = 5000 nstlog = 5000 ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holoyesmic 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 ; 10 fs vdwtype = Switch rvdw-switch = 1.0 rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted potential rcoulomb ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 320.12 320.12 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC gen_temp = 320.12 DispCorr = EnerPres ; account for cut-off vdW scheme gen_seed = 173529 gen_vel = yes ; assign velocities from Maxwell distribution I get the error: step 12005: Water molecule starting at atom 7030 can not be settled. I tried to repeat it and I get the same error with another water molecule at different step. I am using Gmx 4.5.5 I tried minimization many times lowering the maximum force by steepest descent, make the time step 1fs in equilibtration but it does not help. I changed to force field as well and the same is happening. Please, advise. Steven -- 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.