Hi. I've been running some polymer simulations on our cluster and I'm getting this error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
What does this error mean? I imagine it is somehow related to the unit cell. Could the error be related to the fact that the unit cell is rather long (along x axis) but short along the other axis. The thickness of the solvation layer is 2.0 nm, which should be OK. I use the following input: ; Run parameters integrator = md ; leap-frog integrator nsteps = 25000000 ; 2 * 25000000 = 50 ns dt = 0.002 ; 2 fs ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Output control nstxout = 10000 ; save coordinates every 20 ps nstenergy = 1000 ; save energies every 20 ps nstlog = 1000 ; update log file every 20 ps ; Neighbour searching ns_type = grid nstlist = 5 rlist = 1.2 ; short-range neighborlist cutoff (in nm) ; Non-bonded interactions vdw-type = shift rvdw = 1.0 ; short-range van der Waals cutoff (in nm) rvdw-switch = 0.8 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT optimize-fft = yes ; optimize the FFT transforms for the current problem ; Temperature coupling is on for three groups tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = POLYMER Water_CL_NA ; three coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 ; Miscelanous gen_vel = no ; Velocity generation is off dispcorr = no ; account for cut-off vdW scheme ; Center of mass (COM) motion removal ; Reason: these options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 10 comm-mode = Linear comm-grps = POLYMER Water_CL_NA - - - Thanks in advance for any help or advice, Jernej Zidar -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
