[gmx-users] P4_error for extending coarse grained MD simulations

张春雷 chunleizhang.pku at gmail.com
Thu Jun 24 14:40:28 CEST 2010

Dear GMX-users,

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.
Getting Loaded...
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?

Many thanks!

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