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?
See also new example
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#section_1
Mark
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