Hello all,
I have one question about RDF calculation in SMD simulation.
I was trying to perform SMD simulation of system containing a lactic acid and a cycle peptide nanotube, in which lactic acid moves through the nanotube with constant velocity. I have analyzed radial distribution function (RDF) of hydrogen atom of lactic acid in distance r from oxygen atoms of nanotube (there are 80 oxygen atoms along the nanotube). It indicates that the H atom has a first peck at 2 A with probability value is 60 and the second peak is appeared at 6 A with probability of 150. I did not suppose that the probability values would be too high.
Can anyone help me to interpret the high value of probabilities?
Thanks in advance,
Pl read the article
Langmuir. Author manuscript; available in PMC 2009 Dec 16.
Published in final edited form as:
Langmuir. 2008 Dec 16; 24(24): 14115–14124.
PMCID: PMC2771889
NIHMSID: NIHMS86484
Modeling of Peptide Adsorption Interactions with a Poly(lactic acid) Surface
C. P. O'Brien, S. J. Stuart, D. A. Bruce, and R. A. Latour.
I think your background is either hard core Physicist or biologist. The peptide bond is isosteric with the ester bond. Look at the conformation of cyclic peptide----which you have not mentioned( in Biology and chemistry every thing is in nano scale). Try to analyze the possible interactions between the cyclic peptide and lactic acid. Also have a look at the conformation of polyglycolides. Simulations will give only numbers, X-ray will provide coordinates of atoms. It is on the basis of distances between atoms and type of groups involved we classify the interactions. It is only game of interactions. To be on the lighter or more serious life is also game of interactions between molecules.
Dear Marzieh
Knowledge is always for expansion. Pl follow it in life. When one learns the things from scratch it gives more enjoyment.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Peptides