[gmx-users] Do checkpoint files contain energies?

[Justin A. Lemkul]

Andrew DeYoung wrote:
> Hi,
> 
> If you have time, can you please tell me if checkpoint (.cpt) files contain
> data on energies?
> 

Yes, it does.

> 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
> commands:
> 
> ---
> 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?
> 

The checkpoint should be all that is necessary.

> ---
> 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).
> 

What you want is "gmxdump -cp check.cpt" - the very end of the file has all the 
energies, written in a manner similar to how they are present in an .edr file.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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