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 <[email protected]>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 <[email protected]>
----- Original Message -----
From: 张春雷 <[email protected]>
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 <[email protected]>
> 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 <[email protected]>写道：
>
> How about using the last .gro file to continue your simulation?
>
>
>
> 2010/6/24 张春雷 <[email protected]>
> 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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