[gmx-users] P4_error for extending coarse grained MD simulations
张春雷
chunleizhang.pku at gmail.com
Thu Jul 8 21:36:52 CEST 2010
Dear all,
I have post this question about a two weeks ago. During these days, I
followed suggestions from Mark and weixin, but did not fix it. Here, I
repeat it again to seek more help.
I attempt to extend MD simulation for a coarse-grained system. CG models are
in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07.
I tried to use check point file state.cpt to extend my simulation. The mdrun
program can read to the check file. But it reported error like this:
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 check the *state.cpt* file using *gmxdump* and compare it with other
checkpoint files that can be used for extending All-atom simulations. I
found that in the CG check point file, some sections are missing: *box-v
(3x3)* and *thermostat-integral*.
I am not sure whether this missing sections cause my run crash. If it is,
could any one tell me possible reasons that result in the loss of box-v and
thermostat-integral and how to fix the problem?
Your suggestions are greatly helpful and appreciated.
Justin Zhang
在 2010年6月25日 下午4:45，张春雷 <chunleizhang.pku at gmail.com>写道：
> Information shown by gmxcheck:
>
> *Checking file state.cpt*
>
> # Atoms 9817
> Last frame -1 time 360000.000
>
>
> Item #frames Timestep (ps)
> Step 1
> Time 1
> Lambda 1
> Coords 1
> Velocities 1
> Forces 0
> Box 1
>
> *Checking file state_prev.cpt*
>
> # Atoms 9817
> Last frame -1 time 359010.000
>
>
> Item #frames Timestep (ps)
> Step 1
> Time 1
> Lambda 1
> Coords 1
> Velocities 1
> Forces 0
> Box 1
>
> *Checking file md_360ns.trr*
> trn version: GMX_trn_file (double precision)
> Reading frame 0 time 0.000
> # Atoms 9817
> Reading frame 2000 time 300000.000
>
>
> Item #frames Timestep (ps)
> Step 2401 150
> Time 2401 150
> Lambda 2401 150
> Coords 2401 150
> Velocities 2401 150
> Forces 0
> Box 2401 150
>
> Is anything wrong?
>
>
> 2010/6/25 Mark Abraham <mark.abraham at anu.edu.au>
>
>
>>
>> ----- Original Message -----
>> From: 张春雷 <chunleizhang.pku at gmail.com>
>> Date: Friday, June 25, 2010 16:46
>> Subject: Re: [gmx-users] P4_error for extending coarse grained MD
>> simulations
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>
>> > 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.
>>
>> What does gmxcheck say about all the files involved?
>>
>> Mark
>>
>>
>> > 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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>>>>
>>> >
>>> >
>>> > --
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>> >
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