[gmx-users] Dynamics

[jkrieger at mrc-lmb.cam.ac.uk]

No, that's wrong because the box does not exist for the protein and water,
they exist in an infinite lattice so the protein outside the box goes into
the next box and interacts with the water there. This is the same as
interacting with water on the other side of the same box, which is how
it's treated in the simulation calculations.

> 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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