[gmx-users] Extending simulation problem.

Dawid das addiw7 at googlemail.com
Wed Aug 20 12:33:45 CEST 2014

Dear Gromacs experts,

I googled for answer and I found these:

but still I am confused about what happens in my simulation. I did 5 ns
simulation and I would like to add extra 5 ns on top of that so that new
results (energies, temperature, trajectory, etc.) will be appended to
already existing files after first 5 ns simulation. Now I used this command
to run MD simulation for the first time:

\$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e
mCherry7-npt-md.edr > $CURDIR/mCherry7-npt-md.log 2>&1

After this in the same directory I run:

tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr
\$MDRUN -s npt-md-ext.tpr -cpi state.cpt

I tried both state.cpt and prev_state.cpt and the beginning of new
simulation looks exactly the same

that means temperature, energies, etc. are the same as if I started
from 0ns step, not from 5ns step of

previous simulation. What can cause that? Is it because of used files
names or I did something else wrong?

Best wishes,

Dawid Grabarek

More information about the gromacs.org_gmx-users mailing list