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<p style="margin: 0px;">Running several free energy perturbation (FEP) runs to further understand how I should set up my larger production runs and I keep getting errors that I cannot find in the gmx-user email or anywhere specifically online.</p>
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<p style="margin: 0px;">Error 1:</p>
I get this error on three of my four runs.The system is a single rna in a water box. Amber03 and tip3p. Two are cyt an the other two are gua. I get through energy minimization (steep) and I fail on positional restriction sd. I can continue on if I turn -dlb on but I get error 2 below.<br />
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Some interactions seem to be assigned multiple times...<br />
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This seemed to occur after a restart of a failed job due to loss of HDD available space. I am trying to reproduce this error.<br />
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<p style="margin: 0px;">Error 2:</p>
<p style="margin: 0px;">This error only comes up if I turn "-dlb on" in the above step. I get through energy minimisation (steep), positional restraint (sd) and I then fail on step 0 of my production run (sd).</p>
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<p style="margin: 0px;">Getting Loaded...<br />
Reading file monomer_md.tpr, VERSION 4.5.1 (single precision)<br />
Starting 2 threads<br />
Loaded with Money<br />
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Making 1D domain decomposition 2 x 1 x 1<br />
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Back Off! I just backed up dhdl.xvg to ./#dhdl.xvg.1#<br />
starting mdrun 'Protein in water'<br />
625000 steps,   2500.0 ps.<br />
step 0/opt/gridengine/default/spool/compute-0-15/job_scripts/1877: line 50: 28413 Segmentation fault      /home/tjmustard/bin/Gromacs/gromacs-4.5.1-runfolder/bin/g4.5.1-mdrun -v -s monomer_md.tpr -o monomer_md.trr -c monomer_after_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt -dlb no</p>
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<p style="margin: 0px;">Both jobs are running on a linux cluster running SGE. I have had several jobs finish on this cluster with no problems. I am also running a slightly modified 4.5.1 version. The topsort.c file in the source code was missing a line of code and I was getting Improper Dihedral in ip_pert errors. I have run several methane hydration FEP's with very similar results. I am hoping this is a small problem that can be fixed easily.</p>
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<p style="margin: 0px;">Thank you for any assistance,</p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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