[gmx-users] P4_error for extending coarse grained MD simulations
chunleizhang.pku at gmail.com
Fri Jun 25 08:45:06 CEST 2010
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
It works. So the checkpoint file appears to contain some error. But it is
generated by a normally finished production simulation.
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
>> 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!
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before
>> 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
> 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...
More information about the gromacs.org_gmx-users