[gmx-users] Do checkpoint files contain energies?

Andrew DeYoung adeyoung at andrew.cmu.edu
Fri Mar 23 22:13:30 CET 2012


If you have time, can you please tell me if checkpoint (.cpt) files contain
data on energies?

Suppose I have a checkpoint file check.cpt, which I obtained by using the
-cpo flag of mdrun.  Now suppose I want to continue the run using a new .mdp
file (not just extend it,
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations), but
using the same ensemble (NVT) and reference temperature.  If I now use the

grompp -f newgrompp.mdp -c conf.gro -p topol.top -o newrun.tpr -t check.cpt
mdrun -deffnm newrun

where newgrompp.mdp contains "continuation = yes" and "gen_vel = no", will
the energies be continuous across the runs?  Or should I also include the -e
flag in my new call to grompp, in addition to the -t flag?

grompp -f newgrompp.mdp -c conf.gro -p topol.top -o newrun.tpr -t check.cpt
-e ener.edr
mdrun -deffnm newrun

assuming that ener.edr was the energy output from the first mdrun (the
commands for which I am not showing).

When I use "gmxcheck -f check.cpt", I get this output:

# Atoms  6144
Last frame         -1 time  600.000   

Item        #frames Timestep (ps)
Step             1
Time             1
Lambda           1
Coords           1
Velocities       1
Forces           0
Box              1

so it is not clear to me whether the .cpt file contains information about
the energy.  gmxdump will not read checkpoint files (it says "File check.cpt
is of an unsupported type. Try using the command 'less check.cpt'" if I use
"gmxdump -f check.cpt"; when I use "less check.cpt", I just get nonsense
characters as less attempts to read binary).

Thank you very much for your time!

Andrew DeYoung
Carnegie Mellon University

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