[gmx-users] choosing Ensemble for production MD run

[Mark Abraham]

On Tue, Mar 11, 2014 at 1:30 PM, Archana Sonawani-Jagtap <
ask.archana at gmail.com> wrote:

> Hi Everyone,
>
> I would like to know if we can run production MD simulation without
> pressure coupling for protein-ligand simulation?
>

Yes. Whether that will produce something scientifically relevant is up to
you.


> Is it always necessary to have both temperature and pressure coupling in
> the final md run.
>

No, as above.


> I have equilibrated the system with NVT followed by NPT and running the
> simulations using respective cpt files. Will my simulation still have the
> same properties 300K and 1 bar in the final run as I had used cpt file for
> final run  however I have mentioned Pressure coupling as off?
>

If you equilibrate in NPT, and then switch to NVT, then your simulation
will be roughly representative of NPT. The larger it is, the less these
differences matter.

How to decide which ensemble to use?
>

That depends what you are modelling and why, and secondarily on whether a
satisfactory implementation of the desired ensemble exists (generally true
in GROMACS).

Mark


>
>
> Please help.
>
> Archana Sonawani-Jagtap
> Senior Research Fellow,
> Biomedical Informatics Centre,
> NIRRH (ICMR), Parel
> Mumbai, India.
> 9960791339
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