[gmx-users] Fatal error: Failed to lock: md.log. Function not implemented.

Justin Lemkul jalemkul at vt.edu
Tue Apr 30 12:01:29 CEST 2013

On 4/29/13 9:30 PM, maggin wrote:
> Hi,
> when I use GROMACS4.5.5 to do peptid simulation. At NVT step, system is not
> equilibration, so I extend NVT simulation as follows:
> tpbconv -s nvt.tpr  -extend 2000  -o next1.tpr
> mpirun -np 4 mdrun_mpi -reprod  -s next1.tpr -cpi nvt.cpt
> after finish this extending, I got files: traj.trr  state_prev.cpt state.cpt
> md.log ener.edr confout.gro
> Though extending, this system is also not equilibration, so I continue
> extend:
> tpbconv -s next1.tpr -extend 1000  -o next2.tpr
> mpirun -np 4 mdrun_mpi  -reprod  -s next2.tpr -cpi state.cpt
> but it doesn't work, and get:
> Program mdrun_mpi, VERSION 4.5.5
> Source code file: checkpoint.c, line: 1757
> Fatal error:
> Failed to lock: md.log. Function not implemented.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> How could fix it? Thank you very much!

mdrun is trying to append to an existing file named md.log.  Either it is not 
there (i.e. moved or renamed) or has been modified in some way that the 
appending mechanism fails.  The solution is to use -noappend or to make use of 
informative names when running mdrun so you do not recycle default names.  For 

mpirun -np 4 mdrun_mpi -reprod -deffnm next2 -cpi state.cpt

All your output files will be prefixed with "next2" instead of their default 
names.  It may save you some hassle.  Also note that -reprod is mainly for 
debugging purposes.  You're likely losing performance by using it.



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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