<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><BR><BR>Dear Gromacs users</DIV>
<DIV>I run DPPC monolayer on Tip4p2005 water layer system with gromacs 3.3</DIV>
<DIV>I had no problem before but when I run the system with command</DIV>
<DIV>grompp_mpi -c .gro -f .mdp -n .ndx -p .top -o .tpr -np 8</DIV>
<DIV>and then qsub .ll</DIV>
<DIV> </DIV>
<DIV>the run starts but it has break down several times, each ime after for ex 987654 steps or more steps or less.</DIV>
<DIV> </DIV>
<DIV>I get in .o.ii file this message:</DIV>
<DIV> </DIV>
<DIV>----</DIV>
<DIV><FONT color=#00007f>PBS has allocated the following nodes:<BR>cx1-25-8-4<BR>cx1-25-8-4<BR>cx1-25-8-4<BR>cx1-25-8-4<BR>cx1-25-8-4<BR>cx1-25-8-4<BR>cx1-25-8-4<BR>cx1-25-8-4<BR>---<BR>mpiexec.intel -genv I_MPI_DEVICE ssm -genv I_MPI_DEBUG 0 -genv I_MPI_PIN yes -genv I_MPI_PIN_MODE lib -genv I_MPI_FALLBACK_DEVICE disable -genv DAPL_MAX_CM_RETRIES 500 -genv DAPL_MAX_CM_RESPONSE_TIME 300 -genv I_MPI_DAPL_CONNECTION_TIMEOUT 300 -machinefile /tmp/pbs.5455562.cx1/tmp.VRhkM11825 -n 8 -wdir /tmp/pbs.5455562.cx1 mdrun_mpi -v -s topol.tpr -np 8</FONT></DIV>
<DIV><FONT color=#00007f>Job output begins below<BR>-----------------------<BR>mpdallexit: cannot connect to local mpd (/tmp/pbs.5455562.cx1/mpd2.console_dmohamma_110411.074928); possible causes:<BR> 1. no mpd is running on this host<BR> 2. an mpd is running but was started without a "console" (-n option)<BR></FONT>---</DIV>
<DIV>what can be the solvation of the possible problem?</DIV>
<DIV> </DIV>
<DIV>Thanks</DIV>
<DIV>D. Aghaie</DIV>
<DIV> </DIV></td></tr></table>