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

[张春雷]

Could anyone give me more suggestions?

Many thanks!
2010/6/24 张春雷 <chunleizhang.pku at gmail.com>

> 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
> are:
>
> $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!
>
> Justin
>
>
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