[gmx-users] query about structural consistency

[abhisek Mondal]

Hello Mark,
    I guess that's an endless question and will vary based on what kind of
ions used in equilibration. So how do I made a decision that I got the
correct equilibrated structure for my production run ? Is it pressure,
density, temperature convergence or I'm missing something?

On Tue, Mar 21, 2017 at 2:31 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Tue, Mar 21, 2017 at 8:40 AM 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) ?
> >
>
> What is the purpose of doing an equilibration? Is that consistent with
> requiring that nothing changes during the process of equilibration?
>
> Mark
>
>
> > Please be comprehensive. I just need to understand something.
> >
> >
> > Thanks
> >
> > --
> > Abhisek Mondal
> >
> > *Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> > --
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-- 
Abhisek Mondal

*Senior Research Fellow*

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

*Kolkata 700032*

*INDIA*