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
--
========================================
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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