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

张春雷 chunleizhang.pku at gmail.com
Fri Jun 25 10:45:28 CEST 2010 

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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