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

Carsten Kutzner ckutzne at gwdg.de
Fri Jul 9 10:00:34 CEST 2010 

Hi Justin,

what kind of error message do you get if you run this system
on a single core without MPI?

Carsten


On Jul 8, 2010, at 9:36 PM, 张春雷 wrote:

> 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
> > 
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > 
> > 
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > 
> > -- 
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search 
> > before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100709/72b7865a/attachment.html>

More information about the gromacs.org_gmx-users mailing list