[gmx-users] Dynamics

[RAHUL SURESH]

Thank you

But if I am extending my simulation with protein outside the box, then
there will not be any effect of water molecules right.?


On Thu, 26 Jan 2017 at 1:25 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> Hi Rahul,
>
>
>
> The protein being out of the box is not a problem except for visualisation
>
> and some analysis (e.g. RMSD). For continuing the simulation, it is a
>
> completely normal consequence of having periodic boundaries and you
>
> shouldn't worry about it. You can then fIx the protein for visualisation
>
> and analysis separately to running. See
>
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
>
>
> To continue the simulation just use mdrun as normal but with the -cpi
>
> flag. If you want more time than you originally set the mdp to ask for
>
> then use tpbconv (gmx convert_tpr in gromacs 5 and later). See
>
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
>
>
> Best wishes
>
> James
>
>
>
> > 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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> >>
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> >>
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