[gmx-users] P4_error for extending coarse grained MD simulations
chunleizhang.pku at gmail.com
Thu Jun 24 14:40:28 CEST 2010
This is Justin.
I am performing coarse-grained simulation on a protein-lipid bilayer system.
This is a MARTINI CG model.
I have successfully completed a 360ns simulation, during which the time step
is 30 fs.
I would like to extend the simulation to 1micro-second. The commands I used
$tpbconv_mpi_d -s md_360ns.tpr -extend 360000 -o md_720ns.tpr
$mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g
md_360ns.log -cpi state.cpt
However, I received the following message:
Checkpoint file is from part 1, new output files will be suffixed part0002.
Reading file md_720ns.tpr, VERSION 4.0.3 (double precision)
Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010
Loaded with Money
starting mdrun 'Protein in POPE bilayer'
24000000 steps, 720000.0 ps (continuing from step 12000000, 360000.0 ps).
step 12000000, remaining runtime: 0 s
p0_6991: p4_error: interrupt SIGSEGV: 11
I have searched the mail-list, but found no similar report. I also search
through google, but no answer seems satisfactory.
I once performed extending simulation for all atom simulation, and the
method mentioned above worked.
Is anyone familiar with MARTINI CG simulation?
Could you give me some suggestions?
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