[gmx-users] RMSD of interested region?

Seera Suryanarayana palusoori at gmail.com
Tue Sep 20 08:35:19 CEST 2016

Dear gromcas users,

I have done simulations for 100ns for protein of my interest. The protein
length is 197 residues and I fixed the positions one n-terminal residue and
from 28th residue to 197 residues also fixed. My interest of area in
protein is from 2 to 27 residues. Although I have done simulations for
complete length of protein. I just want calculate the RMSD values for
region between 2 to 27. If I use reference structure md_0_1.tpr, it gives
RMSD for entire protein. But how to find RMSD for my interest of region (2
- 27 residues)?   Kindly guide me how to do it.

Thanks in advance
Graduate student

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