Hi!<br>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<br> <br>mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro &<br> <br>I get this error message (below). <span style="color: rgb(0, 0, 0);">My pr.mdp and distance restraints files are given below the error message<br>
. <font size="2"><b><br>Question.</b></font> Ho</span>w 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!!<br>
Please guide. <br>Thanks<br>JJ<br>
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<span style="color: rgb(255, 102, 102);">Back Off! I just backed up md.log to ./#md.log.6#</span><br style="color: rgb(255, 102, 102);"><span style="color: rgb(255, 102, 102);">
Reading file pr.tpr, VERSION 4.0 (single precision)</span><br style="color: rgb(255, 102, 102);">
<br style="color: rgb(255, 102, 102);"><span style="color: rgb(255, 102, 102);">
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)
</span><br style="color: rgb(255, 102, 102);">
<br style="color: rgb(255, 102, 102);">
<br style="color: rgb(255, 102, 102);"><span style="color: rgb(255, 102, 102);">
WARNING: Can not write distance restraint data to energy file with domain decomposition</span><br style="color: rgb(255, 102, 102);">
<br style="color: rgb(255, 102, 102);"><span style="color: rgb(255, 102, 102);">
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Program mdrun_mpi, VERSION 4.0.2 </span><br style="color: rgb(255, 102, 102);"><span style="color: rgb(255, 102, 102);">
Source code file: domdec.c, line: 5842 </span><br style="color: rgb(255, 102, 102);">
<br style="color: rgb(255, 102, 102);"><span style="color: rgb(255, 102, 102);">
Fatal error:</span><br style="color: rgb(255, 102, 102);"><span style="color: rgb(255, 102, 102);">
There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 9.85926 nm</span><br style="color: rgb(255, 102, 102);"><span style="color: rgb(255, 102, 102);">
Change the number of nodes or mdrun option -rdd or -dds </span><br style="color: rgb(255, 102, 102);"><span style="color: rgb(255, 102, 102);">
Look in the log file for details on the domain decomposition </span> <br>
-----------------------------------------------------------------------------------------------------------------------------------------------<br><br><span style="color: rgb(51, 102, 255);"></span><font size="4"><b>pr.mdp</b></font><br>
<br>; User spoel (236)<br>; Wed Nov 3 17:12:44 1993<br>; Input file<br>;<br>title = Yo<br>cpp = /usr/bin/cpp<br>define = -DDISRES<br>constraints = none<br>
;constraint_algorithm = lincs<br>;lincs_order = 4<br>integrator = md<br>dt = 0.001 ; ps !<br>nsteps = 4000000 ; total 2.0ns.<br>nstcomm = 1<br>nstxout = 50000<br>
nstvout = 50000<br>nstfout = 50000<br>nstlog = 50000<br>nstenergy = 500<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>
rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>
ewald_rtol = 1e-5<br>optimize_fft = yes<br>disre = simple<br>disre_weighting = equal<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = V-rescale<br>tc-grps = Protein Non-Protein<br>
tau_t = 0.1 0.1<br>ref_t = 300 300<br>; Energy monitoring<br>energygrps = Protein Non-Protein<br>;tnc Non-Protein tnt NMR tni<br>; Pressure coupling is not on<br>Pcoupl = parrinello-rahman<br>
tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>;simulated annealing<br>;Type of annealing form each temperature group (no/single/periodic)<br>;annealing = no, no, no, single, no<br>
;<br>;Number of annealing points to use for specifying annealing in each group<br>;annealing_npoints = 0, 0, 0, 9, 0<br>;<br>; List of times at the annealing points for each group<br>;annealing_time = 0 25 50 75 100 125 150 175 200<br>
; Temp.at each annealing point, for each group.<br>;annealing_temp = 300 350 400 450 500 450 400 350 300<br><br><b><font size="4"><br><span style="color: rgb(51, 102, 255);"> distance restraints file</span></font></b><br>
<br> distance_restraints ]<br>; ai aj type index type' low up1 up2 fac<br>;TnT240-TnI131, 145, 151, 160, 167 (ca+-7)<br> 2019 3889 1 1 1 3.91 3.91 5.31 0.574679<br>
2019 4056 1 2 1 4.86 4.86 6.26 0.409911<br> 2019 4133 1 3 1 5.69 5.69 7.09 0.457947<br> 2019 4207 1 4 1 6.63 6.63 8.03 0.323852<br>
2019 4273 1 5 1 7.14 7.14 8.54 0.294559<br>;TnT276- Tni 131,145,151,160,167,5,17,27,40<br> 2434 3889 1 6 1 1.34 1.34 2.74 4.884769<br> 2434 4056 1 7 1 2.13 2.13 3.53 0.523368<br>
2434 4133 1 8 1 3.66 3.66 5.06 0.409911<br> 2434 4207 1 9 1 4.48 4.48 5.88 0.547825<br> 2434 4273 1 10 1 5.43 5.43 6.83 0.285938<br>
2434 2628 1 11 1 5.89 5.89 7.29 0.241333<br> 2434 2719 1 12 1 4.76 4.76 6.16 0.366358<br> 2434 2824 1 13 1 3.81 3.81 5.21 0.644145<br>
2434 2972 1 14 1 3.10 3.10 4.50 0.431009<br>;TnT288- Tni 131,145,151,160,167,5,17,27,40<br> 2557 3889 1 15 1 1.89 1.89 3.29 1.429688<br> 2557 4056 1 16 1 3.25 3.25 4.65 0.32931<br>
2557 4133 1 17 1 4.44 4.44 5.84 0.346847<br> 2557 4207 1 18 1 4.80 4.80 6.20 0.275198<br> 2557 4273 1 19 1 5.84 5.84 7.24 0.200744<br>
2557 2628 1 20 1 4.79 4.79 6.19 1.046736<br> 2557 2719 1 21 1 5.06 5.06 6.46 0.267659<br>; 2557 2824 1 22 1<br> 2557 2972 1 23 1 3.99 3.99 5.39 0.412797<br>
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