Hi! I am performing an mpi MD (on a quad core system) run with distance restraints. When I execute this command below without position restraints the MD run is distributed over 4 nodes perfectly well. But when I incorporate the distance restraints I hit a road block
mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro & I get this error message (below). My pr.mdp and distance restraints files are given below the error message . * Question.* How do I handle this sitation? Do I increase the long range cut off in the pr.mdp file? If you see my distance restraints file, my upper range of distances are close to 9nm!! Please guide. Thanks JJ ---------------------------------------------------------------------------------------------------------------------------------------------------------- Back Off! I just backed up md.log to ./#md.log.6# Reading file pr.tpr, VERSION 4.0 (single precision) NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd) WARNING: Can not write distance restraint data to energy file with domain decomposition ------------------------------------------------------- Program mdrun_mpi, VERSION 4.0.2 Source code file: domdec.c, line: 5842 Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 9.85926 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition ----------------------------------------------------------------------------------------------------------------------------------------------- *pr.mdp* ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DDISRES constraints = none ;constraint_algorithm = lincs ;lincs_order = 4 integrator = md dt = 0.001 ; ps ! nsteps = 4000000 ; total 2.0ns. nstcomm = 1 nstxout = 50000 nstvout = 50000 nstfout = 50000 nstlog = 50000 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes disre = simple disre_weighting = equal ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ;tnc Non-Protein tnt NMR tni ; Pressure coupling is not on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ;simulated annealing ;Type of annealing form each temperature group (no/single/periodic) ;annealing = no, no, no, single, no ; ;Number of annealing points to use for specifying annealing in each group ;annealing_npoints = 0, 0, 0, 9, 0 ; ; List of times at the annealing points for each group ;annealing_time = 0 25 50 75 100 125 150 175 200 ; Temp.at each annealing point, for each group. ;annealing_temp = 300 350 400 450 500 450 400 350 300 * distance restraints file* distance_restraints ] ; ai aj type index type' low up1 up2 fac ;TnT240-TnI131, 145, 151, 160, 167 (ca+-7) 2019 3889 1 1 1 3.91 3.91 5.31 0.574679 2019 4056 1 2 1 4.86 4.86 6.26 0.409911 2019 4133 1 3 1 5.69 5.69 7.09 0.457947 2019 4207 1 4 1 6.63 6.63 8.03 0.323852 2019 4273 1 5 1 7.14 7.14 8.54 0.294559 ;TnT276- Tni 131,145,151,160,167,5,17,27,40 2434 3889 1 6 1 1.34 1.34 2.74 4.884769 2434 4056 1 7 1 2.13 2.13 3.53 0.523368 2434 4133 1 8 1 3.66 3.66 5.06 0.409911 2434 4207 1 9 1 4.48 4.48 5.88 0.547825 2434 4273 1 10 1 5.43 5.43 6.83 0.285938 2434 2628 1 11 1 5.89 5.89 7.29 0.241333 2434 2719 1 12 1 4.76 4.76 6.16 0.366358 2434 2824 1 13 1 3.81 3.81 5.21 0.644145 2434 2972 1 14 1 3.10 3.10 4.50 0.431009 ;TnT288- Tni 131,145,151,160,167,5,17,27,40 2557 3889 1 15 1 1.89 1.89 3.29 1.429688 2557 4056 1 16 1 3.25 3.25 4.65 0.32931 2557 4133 1 17 1 4.44 4.44 5.84 0.346847 2557 4207 1 18 1 4.80 4.80 6.20 0.275198 2557 4273 1 19 1 5.84 5.84 7.24 0.200744 2557 2628 1 20 1 4.79 4.79 6.19 1.046736 2557 2719 1 21 1 5.06 5.06 6.46 0.267659 ; 2557 2824 1 22 1 2557 2972 1 23 1 3.99 3.99 5.39 0.412797
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