Dear gmx-users, I am heating my system at 300 K.
I have set the pbc conditions as "no" I get the following error: ------------------------------------------------------- Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 5436 Fatal error: pbc type no is not supported with domain decomposition, use particle decomposition: mdrun -pd ------------------------------------------------------- I tried looking for a similar option as "-pd" for parallel runs, but could not find any. The md.mdp is: ; Run parameters integrator = md ; leap-frog integrator nsteps = 500000 ; 2 * 500000 = 1000 ps, 1 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 NPT 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 ; search neighboring grid cells 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 = 400 400 ; 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 Kindly guide regarding this. Thanks, SN
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