I have studied the structural changes of a protein in 3 different concentrations of ionic liquids (50 mM, 500 mM, and 1M). On analysis of the RDF plots, I find that the magnitude of the RDF plot for the anion at 0.35 nm from the protein followed the order 50 mM > 500 mM > 1M (as seen in the attached images). The magnitude of the plot is also very high at 50 mM (~ 60). However, on visualizing the trajectories, I can see that only at 1 M concentration, there is an increased concentration of the ions in the solvation shell of the protein, and at 50 mM, there are very few ions surrounding the protein. What could be the reason for such high g(r) values at lesser concentrations of 50 mM and 500 mM?
I used "gmx_mpi rdf com rdf mol_com -s em.tpr -f md_Dhp1M.xtc -cn -o ranion_Run2.xvg -tu ns -dt 100 -cut 0.35" for the analysis.
Thanks.
Dear Vidya
I found that you calculated RDF of protein respect to anions,
How many atoms does the protein have?
if your protein is large, it is better to calculate RDF for special residues
Also, you could use analysis such as RMSD, RMSF, and DSSP for detecting a change in protein structure.
Hope it helps
Azadeh Kordzadeh Thanks for your reply.
Yes, you are right these are the plots of the anions. The protein is insulin which has only 51 amino acids and I have calculated the RDF for a specific N-terminal residue (Phenylalanine). I have also calculated the RMSD, RMSF etc.
Would like to know the reason for the discrepancy with respect to RDF and concentration of the anions.
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