I have run REMD (replica exchange molecular dynamic) simulations of a dimer. I want to do 3 different types of clustering based on:
1. The RMSD (Root Mean Square Distance) between chain A and chain B.
2. RMSD of Chain A only.
2. RMSD of Chain B only.
How to do this using gmx cluster and what are the selections that are to be given in least square fit and RMSD calculation?
You've to make separate index files for the dimer, chain A and chain B, then use "gmx cluster". Details: https://manual.gromacs.org/documentation/2018/onlinehelp/gmx-cluster.html
You may also try this tool for RMSD based clustering: https://tubiana.me/research/ttclust/
Sutanu Mukhopadhyay If I want to do clustering for dimer based on the RMSD between chain A and chain B and not within chain A and chain B itself. Then what should be the least square fitting and rmsd option to be choosen?
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