[gmx-users] Extending run using tpbconv and mdrun

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 19 10:43:22 CEST 2012

On 19/04/2012 6:16 PM, D_Roy wrote:
> Hi,
> I am trying to do a simulation of 10ns of protein in water. Due to the
> limitations in my computer speed, I have decided to break it up in 5 days
> with 2ns run per day.
> For the first 2ns run I have used the commands:
> mdrun -v -deffnm protein_previous
> I went through the gromacs documentation and tried the following method to
> do an extended run of 2ns after the first day:
> tpbconv -s protein_previous.tpr -extend 2000 -o protein_next.tpr
> mdrun -s protein_next.tpr -cpi protein_previous.cpt -cpo protein_next.cpt
> It worked for the first extended simulation giving me the output files:
> confout.gro ; ener.edr ; traj.xtc ; traj.trr ; md.log
> When I try the same steps for 2ns for the third time with the commands:
> tpbconv -s protein_next.tpr -extend 2000 -o protein_another.tpr
> mdrun -s protein_another.tpr -cpi protein_next.cpt -cpo protein_another.cpt
> It start from the beginning.
> > From the mailing lists, I could guess it may be that mdrun cannot find the
> checkpoint file previous_next.cpt. But the filename is correct. So why is it
> starting from the begining?

Look in the .log file for what mdrun thought about the (default) request 
for appending to previous output files.


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