Dear gmx-users,<br><br>I am heating my system at 300 K.<br><br>I have set the pbc conditions as "no"<br><br>I get the following error:<br>-------------------------------------------------------<br>Program mdrun_mpi, VERSION 4.0.5<br>
Source code file: domdec.c, line: 5436<br><br>Fatal error:<br>pbc type no is not supported with domain decomposition,<br>use particle decomposition: mdrun -pd<br>-------------------------------------------------------<br>
<br>I tried looking for a similar option as "-pd" for parallel runs, but could not find any.<br><br>The md.mdp is:<br>; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 500000 ; 2 * 500000 = 1000 ps, 1 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 NPT<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>ns_type = simple ; search neighboring grid cells<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 = 400 400 ; 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>pbc = no ; 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>Kindly guide regarding this.<br><br>Thanks,<br>SN<br><div style="visibility: hidden; left: -5000px; position: absolute; z-index: 9999; padding: 0px; margin-left: 0px; margin-top: 0px; overflow: hidden; word-wrap: break-word; color: black; font-size: 10px; text-align: left; line-height: 130%;" id="avg_ls_inline_popup">
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