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.
Mark
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