Dear gmx-users,<br><br>I have a cube (8 nm) of the system containing 1:1 :: water: methanol, a polypeptide, Li ions and 2,5-dihydroxybenzoic acid anions.<br>I am heating this system with no PBC ( evaporation). <br><br>The md.mdp file is:<br>
<br>; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 250000 ; 2 * 250000 = 500 ps, 0.5 ns<br>dt = 0.002 ; 2 fs<br>; Output control<br>nstxout = 1000 ; save coordinates every 2 ps<br>
nstvout = 1000 ; save velocities every 2 ps<br>nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps<br>nstenergy = 1000 ; save energies every 2 ps<br>nstlog = 1000 ; update log file every 2 ps<br>
; Bond parameters<br>continuation = yes ; Restarting after NVT<br>constraint_algorithm = lincs ; holonomic constraints<br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>lincs_iter = 1 ; accuracy of LINCS<br>
lincs_order = 4 ; also related to accuracy<br>; Neighborsearching<br><b>ns_type = simple </b> <br>nstlist = 5 ; 10 fs<br>rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br>
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>; Electrostatics<br>;coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>;pme_order = 4 ; cubic interpolation<br>;fourierspacing = 0.16 ; grid spacing for FFT<br>
; Temperature coupling is on<br>tcoupl = V-rescale ; modified Berendsen thermostat<br>tc-grps = Protein Non-Protein ; two coupling groups - more accurate<br>tau_t = 0.1 0.1 ; time constant, in ps<br>ref_t = 500 500 ; reference temperature, one for each group, in K<br>
; Pressure coupling is on<br>pcoupl = no<br>pcoupltype = isotropic ; uniform scaling of box vectors<br>tau_p = 2.0 ; time constant, in ps<br>ref_p = 1.0 ; reference pressure, in bar<br>compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1<br>
; Periodic boundary conditions<br><b>pbc = no </b> ; 3-D PBC<br>; Dispersion correction<br>DispCorr = no ; account for cut-off vdW scheme<br>; Velocity generation<br>gen_vel = no ; Velocity generation is off<br>
;comm_mode<br>comm_mode = ANGULAR<br><br><br>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 <b>( interactive runs fine)</b><br>
<br><br>Fatal error:<br>Domain decomposition does not support simple neighbor searching, use grid searching or use particle decomposition<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
<br><br>With pbc = no the only grid type an be used is simple.<br>I tried changing the size of the cube but I still face the same problem.<br><br>I am unable to understand what could be going wrong suddenly.<br><br>Please guide<br>
<br>Thanks in advance,<br>SN<br><br><br><br>