[gmx-users] query about structural consistency

abhisek Mondal abhisek.mndl at gmail.com
Tue Mar 21 13:18:58 CET 2017

I really appreciate your thoughts. I know about the words like "exact" or
"correct" does not stand in such scenario. I just needed an expert opinion
regarding the quality assurance of the equilibrated structure. People often
tend to ask question like how can you say that your model is properly
equilibrated to perform a production MD, we are all more or less familier
with that.

Thanks again for the comment.

Best regards,

On Tue, Mar 21, 2017 at 5:26 PM, Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk
> wrote:

> 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.
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Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*


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