[gmx-users] Dynamics

[RAHUL SURESH]

Hi mark

I want to extend it for another 50ns. At 100ns protein is out of the box.
Now is t possible to apply boundary conditions and extend.?



On Wed, 25 Jan 2017 at 11:12 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
>
>
> 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.
>
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
>
>
>
>
> > 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
>
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
>
>
> 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.
>
>
>
> Mark
>
>
>
> waiting for your valuable note.
>
> > --
>
> > *Regards,*
>
> > *Rahul Suresh*
>
> > *Research Scholar*
>
> > *Bharathiar University*
>
> > *Coimbatore*
>
> > --
>
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