[gmx-users] Extending run using tpbconv and mdrun

D_Roy r.dipankar at gmail.com
Thu Apr 19 10:16:50 CEST 2012


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?

Would appreciate if someone can help me out.

Dipankar Roy

Research Assistant
Sikkim Manipal University DE

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