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

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

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