[gmx-users] query about structural consistency

[Hannes Loeffler]

On Tue, 21 Mar 2017 13:09:46 +0530
abhisek Mondal <abhisek.mndl at gmail.com> wrote:

> Hi,
> 
>     I just have a basic query.
> 
>     I'm working with a protein-ligand system with a goal of performing
> Umbrella sampling in gromacs. So first, after I build the complex, I'm
> going for NVT and followed by NPT equilibration of 20ns each. After
> equilibration, is it mandatory that my equilibrated protein-ligand
> complex matches exactly with the crystal structure used for
> equlibration (I mean before and after) ?
> 
> Please be comprehensive. I just need to understand something.

It's easy to ask for a "comprehensive" answer on a mailing list but
what you need to realise is that you are really asking about is the
basics of molecular simulation.  There is no quick answer to this and
whole text books have been written on the topic.

The way "equilibration" is typically used is to really mean to reach a
nearby local minimum and expect to see a convergent behaviour with
respect to a chosen target property.  This paper,
dx.doi.org/10.1021/acs.jctc.5b00784 may be an interesting starting
point.

You may also want to abandon words like "exact" or "correct" in this
context.


Cheers,
Hannes.