Luís Pereira wrote:
Hi Justin,
Thank you for your quick answer.
All the files are in the working directory but have different names,
e.g., the .trr is not traj.trr but 7fboh3.trr, and so on.
If you do not supply filenames, then the defaults are assumed. This is true of
all Gromacs programs.
I've backed up the working directory, run gromacs with all output file
names written in command line and now everything is working fine:
1000000 steps, 1000.0 ps (continuing from step 878000, 878.0 ps).
Well, i'll have to wait to see if the final results are ok.
They should be, provided the command issued is correct.
-Justin
Luís
On 8 August 2011 21:47, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Luís Pereira wrote:
Hi all,
I'm trying to restart a simulation from a power source failure,
but mdrun complains about a missing .trr file:
Program mdrun, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/gmxfio.__c, line: 737
Can not open file:
traj.trr
The manual says that there is no need to supply more information
than:
mdrun -s topol.tpr -cpi state.cpt -append
Do I have to write all the output files in the above command
line? Or there was something wrong when gromacs wrote the
checkpoint file?
If you're appending, then all the expected files must be present in
the working directory, unmodified. It appears that this is not the
case, as traj.trr is missing. You can always use -noappend and
concatenate any relevant output later.
-Justin
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==============================__==========
Justin A. Lemkul
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Virginia Tech
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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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