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

[张春雷]

The last .gro file only provides coordinates of the system. No velocity is
recorded. Actually, what I attempt to achieve is a binary identical
trajectory. So I think the velocity from the last step is critical.

I have tried another approach in which the checkpoint file is neglected.

$mdrun_mpi_d -s md_720ns.tpr  -e md_720ns.edr -o md_720ns.trr -g
md_720ns.log

It works. So the checkpoint file appears to contain some error. But it is
generated by a normally finished production simulation.
Have  you encountered similar things?

Thank you for your suggestions!



在 2010年6月25日 上午9:16，weixin <xwxnju at gmail.com>写道：

>
> How about using the last .gro file to continue your simulation?
>
>
>
> 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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