[gmx-users] Resuming of calculation from last *.cpt

Justin Lemkul jalemkul at vt.edu
Sat Sep 15 19:33:55 CEST 2012

On 9/15/12 10:33 AM, James Starlight wrote:
> There is no errors in the filenames
> In the above example init and initial names were used for simplicity :)

What you accomplished was confusion.  Always use real file names.  If you know 
enough to filter information and create a false reality, you'd probably be able 
to solve the issue without us ;)

> Actually the name of the simulation was md_a2a_pope_SD
> so I've used
> mpiexec -np 48 mdrun_mpi.openmpi -v -cpi md_a2a_pope_SD -deffnm
> md_a2a_pope_SD -append
> and eror was
> Fatal error:
> Failed to lock: md_a2a_pope_SD.log. Already running simulation?
> from cpt file after dump
> output filename = md_a2a_pope_SD.log

I have seen this sometimes for unknown reasons.  The solution is to use 
-noappend and concatenate later.  Using the .cpt file guarantees a faithful 
continuation of the job; that's what is most important.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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