[gmx-users] Running long MD simulation

Justin Lemkul jalemkul at vt.edu
Sun Feb 4 15:19:51 CET 2018

On 2/4/18 9:15 AM, Ahmed Mashaly wrote:
> Thanks Justin.
> I found this one:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118282.html
> Another question I have about using cpt
> I know checkpoint is important for continuing simulation, but I didn't know that we have to use it also from nvt output to npt input and from npt output to md input ... I was just using the output .gro as input for the next step ... Is this a fatal mistake?

Checkpoint files are essential for exact continuations. Without them, 
you lose thermodynamic state information, precise velocities, etc. 
Always use a checkpoint.

> If I have to use it then I can use it with grompp -t prev_checkpoint.cpt or with mdrun -cpi prev_checkpoint.cpt ... Would it be the same result?

You only need to invoke grompp if changing something about the system - 
output settings, ensemble, use of restraints, etc. Otherwise, just 
extend via convert-tpr and mdrun -cpi.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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