[gmx-users] MD simulations of two chains protein

Khadija Amine kh.amine1 at gmail.com
Mon Nov 14 12:33:35 CET 2016

Dear Gromacs users,

I need your help regarding MD simulation of two chains protein.
The chain A is 2-78 aa, and the chain B is 1-168 aa.

I started with the pdb file where there is specified names of the two
chains as A and B.

I did solvation of my system in a cubic box, I tried to open the pdb file
issued from this step I didn't find the column specifying the chain names.

I run 20 ns of MD for this protein. The RMSF plot of the protein seems to
be overlapping from 1 to 78 and the rest of the residues flctuation is good.

As it is the first time am facing such issues with protein with two chains,
how can I avoid such overlap in RMSF plot?

Is this linked to the chains numbering issued after writing the topology.

Thank you

*Khadija AMINE*

*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

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