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

[Mark Abraham]

----- 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100625/9108184e/attachment.html>