Dear gmx-users, I have a cube (8 nm) of the system containing 1:1 :: water: methanol, a polypeptide, Li ions and 2,5-dihydroxybenzoic acid anions. I am heating this system with no PBC ( evaporation).
The md.mdp file is: ; Run parameters integrator = md ; leap-frog integrator nsteps = 250000 ; 2 * 250000 = 500 ps, 0.5 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NVT 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 = simple * nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) 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 = 500 500 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = no 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 ; Periodic boundary conditions *pbc = no * ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ;comm_mode comm_mode = ANGULAR I have run this system in past without any errors, suddenly I am constantly running into the following error if I submit my job on a cluster in que *( interactive runs fine)* Fatal error: Domain decomposition does not support simple neighbor searching, use grid searching or use particle decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors With pbc = no the only grid type an be used is simple. I tried changing the size of the cube but I still face the same problem. I am unable to understand what could be going wrong suddenly. Please guide Thanks in advance, SN
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