[gmx-users] query about structural consistency
mark.j.abraham at gmail.com
Tue Mar 21 10:01:46 CET 2017
On Tue, Mar 21, 2017 at 8:40 AM abhisek Mondal <abhisek.mndl at gmail.com>
> 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?
> Please be comprehensive. I just need to understand something.
> Abhisek Mondal
> *Research Fellow*
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
> *Kolkata 700032*
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