I am trying using prev_md.cpt file. I checked and it looks okay, so
hopefully it will work. If not I will try using .trr files.
Thanks
Quoting Tsjerk Wassenaar <[email protected]>:
Hey,
Otherwise it's also still possible to do old style continuation with a
frame from the .trr/.edr file, provided you have those...
Cheers,
Tsjerk
On Thu, Apr 22, 2010 at 7:55 PM, Justin A. Lemkul <[email protected]> wrote:
[email protected] wrote:
Hi Justin,
Well the way I continued my second part of the simulation was using my
md.cpt file. I checked my .cpt file and this is what I got:
Last frame -1 time 83786.961 , so I guess my second run updated
the file, so does this mean I have to do the whole simulation again? or can
I use any of the other files for example .trr file? I thought it might be
that I don't have enough disk space?
Checkpoint files will over-write each other, but a backup is kept as
(whatever)_prev.cpt; you may be able to use this file to re-start your run.
If md.cpt corresponds to a time where there is a viable frame in your
trajectory, then there should be no problem re-starting it from this .cpt
file. That is, if the frame at (or after) 83790 is corrupt, re-starting
from time 83786 should present no problem.
Maybe you're out of disk space, but only you know if that's the problem :)
-Justin
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Hello,
I am running simulations and I got Magic Number error: Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)
Checking file md.part0002.xtc
Reading frame 0 time 48190.004
# Atoms 6533
Precision 0.001 (nm)
Reading frame 178000 time 83790.008
Part one of the simulation ran fine, but it exceeded the run time so I
ran it again, and got part0002.xtc file. Now it seems like my
part0002.xtc
file is corrupted, is there a way I can just run my simulation
again from
my first file without running the whole thing again?
That's the nice part about checkpointing. As long as you have the .cpt
file from wherever you started the continuation, you can just re-run
from that same point. That's really what you did in the first place.
If, for some reason, you've over-written or deleted that .cpt file,
then you can only start from some later .cpt file, or in the worst
case, all over again.
-Justin
Thanks.
N.P
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
--
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
