[gmx-users] can not restart a simulation from the checkpoint file

[Justin A. Lemkul]

Chen, Zhihong (chenz2) wrote:
> Hi, I runed 2 ns membrane simulations. But I cann't restart these simulations
> using the checkpoint file, The error message is   Warning: task died with
> signal 11 (Segmentation fault). Since the trr file include the force,

What was your exact command?

> velocity information of atoms, so I restarted the simulations from trr file
> and it works. But when I tried to visionize the trr file in VMD, I saw weird
> long lines between atoms across the cell box. I think that is because  atoms
> are swithing from one periodic box to another. So the bond information are
> messed up when shown in VMD.  What I am concerned is , is there a problem to
> restart simulations from trrr file? And how to restart from cpt file, solving
> that Segmentation Fault? Could someone give me help on this? Thanks chen
> 

Without seeing the command you provided, there's no way to tell.  There is a 
how-to for doing restarts on the Gromacs website.  The weird bonds you're seeing 
are a normal consequence of PBC, nothing to worry about (again, see the website 
for more details).

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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