[gmx-users] Dynamics

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

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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