[gmx-users] how to modify the code to generate more controllable checkpoints to restart?

[Yong Wang]

Hi,

I'd like to restart the MD simulation from some time points (e.g. 10ns
before the end) but with minorly adjusted parameters. But it seems the
current Gromacs code can't do this right now.

I am trying to understand how the checkpoints in gromacs work. But I only
found very limited document about it:
"The checkpoint file is by default written to disc every 15 minutes (and
always at the very end of a simulation), and it contains the latest
full-precision velocities, forces, and energies that are required to
continue a simulation, or restart a crashed-simulation. "

Is it possible that we can control the output of checkpoint files as
flexibly as other files (e.g. .xtc or .edr) by introducing some mdp
options? More concretely, like using nstcptout=1000000 to write the
checkpoint files every 2ns with a suffix of md.cpt_${step}. I guess I have
to do some coding, but don't know if there will be too much work. Could
anyone show some guidance on this? Thanks.

Yong

-- 

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Yong Wang
PhD Student, Structural Biology and NMR Laboratory (SBiNLab)
Department of Biology, University of Copenhagen, Denmark
Ole Maaloes Vej 5, DK-2200 Copenhagen N
https://www.researchgate.net/profile/Yong_Wang15