[gmx-users] Running long MD simulation
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:
> 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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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