[gmx-users] query about structural consistency

abhisek Mondal abhisek.mndl at gmail.com
Tue Mar 21 08:39:49 CET 2017


    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.


Abhisek Mondal

*Research Fellow*

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

*Kolkata 700032*


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