How can we calculate rmsf value of protein-ligand complex in md simulation of protein-ligand complex in gromacs? What would be its significance in case md of drug-protein complex?
What other analysis can be performed and what commands can be used?
Thanking in advance.
Sutanu Mukhopadhyay
- For rmsf plot and calculation, you can use the following command:
gmx rmsf -f md_protein.xtc -s md_protein.pdb -o rmsf.x
- RMSF (Root Mean Square Fluctuation) is a measure of average movement of atomic positions with respect to time. It can be mesured by capturing the sum of total positional displacement of atom for each conformation generated, then averaged by the number of conformations.
- Depending on your research questions, various analyses can be done such as RMSD, RMSF, Radius of Gyrartion, SASA, PCA, hydrogen bonding etc. You can get an overview here: http://www.strodel.info/index_files/lecture/html/analysis-1.html
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