[gmx-users] query about structural consistency

[Mark Abraham]

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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