[gmx-users] Dynamics

Mark Abraham mark.j.abraham at gmail.com
Wed Jan 25 18:42:26 CET 2017


On Wed, 25 Jan 2017 18:00 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> from production output of a monomer for 100ns, there s a instability in the
> structure from 83ns to 100ns.

Many things could be going on here...

Also .gro file shows, the protein is out of
> the cube.

Mdrun doesn't care. There's infinitely many equivalent representations of a
periodic system.

> gmx make_ndx -f md.gro -o index.ndx
> trjconv -f md.xtc -s md.tpr -n index.ndx -pbc mol -ur compact -center -o
> outputfile.xtc
> I used the above commands to bring the protein to the center of the box.
> gmx trjconv -f outputfile.xtc -s md.tpr -o newmd.trr
> And using the above command, extracted a trr file.
> Now can I extend this job with this trr file as it is or should i give any
> periodic boundary conditions or should take the conformer structure at 80ns
> and run for another 50ns?

None of this is needed. See

Whether it makes sense to try to repeat or extend or go back to the start
and try to fix something depends on what the "instability" is, and what is
causing it.


waiting for your valuable note.
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
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