Dear GMXers my mdrun stops when I try to do it with 8 nodes, but there's no error message, here's the end of the md0.log:
"B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 -------- -------- --- Thank You --- -------- -------- Initializing LINear Constraint Solver number of constraints is 3632 average number of constraints coupled to one constraint is 2.9" I also tried 6 nodes or 10 nodes, but mdrun always stops here, there's no problem if I ran it by -np 4. I searched the list, I found some people said that this probably because the MPI version, currently, we used the 1.2.7 It is weird that another cluster, install mpich1.2.7, goes well with mdrun. I also installed mpich2 in my personal directory (I have no administrator privilege on the cluster...), but it keeps on complaining the "mpd" setting, though I created a .mpd.conf file as it told me in my home directory. Should I install mpich2 by root? Is there any conflict if I installed both mpich1 and mpich2? I've searched the list but cant find something useful to solve my problem Any suggestions will be REALLY appreciated! Xin Liu
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