<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:12pt;color:#000000;"><div>Hi everyone;<br><br>I am trying to do some simulation using frozen groups on an 8 core computer. I have tow boxes: <br><br>1) Box 1 has two proteins and both of them are kept frozen (I used [exclusions] directive in topology file to exclude the interactions in each frozen group, NVT). <br><br>2) Box 2 has those two proteins but without being frozen (no use of [exclusions] and freeze options). <br><br>Here is the mdp file:<br>=========================================================<br>integrator = sd<br>dt = 0.002<br>nsteps = 50000<br>comm_mode =
None<br>ns_type = grid<br>pbc = xyz<br>nstlist = 10<br>rlist = 1<br>coulombtype = PME<br>rcoulomb = 1<br>fourierspacing = 0.12<br>pme_order = 6<br>ewald_rtol = 1e-6<br>vdwtype = Switch<br>rvdw_switch = 0.8<br>rvdw = 0.9<br>DispCorr = EnerPres<br>nstxout =
500<br>nstvout = 500<br>nstlog = 500<br>nstenergy = 500<br>nstxtcout = 5000<br>xtc-precision = 1000<br>tc_grps = system<br>tau_t = 1<br>ref_t = 310<br>energygrps = chainC chainF SOL ; these three lines were commented out for the box 2 simulation<br>freezegrps = chainC
chainF<br>freezedim = Y Y Y Y Y Y<br>=========================================================<br><br><br><br><br>I used this command to run the simulations:<br>mpiexec -n 8 mdrunmpi -s eqvspc.tpr -c eqvspc.gro -o eqvspc.trr -x eqvspc.xtc -g eqvspc.log -e eqvspc.edr<br><br>It works for the box two (no freeze), but for box 1 gives me this error:<br>=========================================================<br>Back Off! I just backed up eqvspc.log to ./#eqvspc.log.11#<br>Reading file eqvspc.tpr, VERSION 4.0.3 (single precision)<br>-------------------------------------------------------<br>Program mdrunmpi, VERSION 4.0.3<br>Source code file: domdec.c, line: 5858<br><br>Fatal error:<br>There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.25692 nm<br>Change the number of nodes or mdrun option -rdd or -dds<br>Look in the log file for details on the domain
decomposition<br>-------------------------------------------------------<br>Error on node 0, will try to stop all the nodes<br>Halting parallel program mdrunmpi on CPU 0 out of 8<br>==========================================================<br><br>The serial version of mdrun works with box 1.<br>I searched the user mailing list and found that some people had similar problem with restraints in the past. I tried to use some -rdd and -dds values, but without any success. Can you please point out where is the source of this error and how I can get domain decomposition and frozen (or restraint) groups to work.<br><br>Any help or hint is highly appreciated!<br><br>Reza Salari<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br></div></div><br>
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