Tutorial_6_5C2H6_pmf

# Tutorial_6_5C2H6_pmf - Oscar Tutorial 6 page 1 Tutorial 6...

This preview shows pages 1–2. Sign up to view the full content.

Oscar Tutorial 6 page 1 Tutorial 6: Ethane Potentials of Mean Force The Boltzmann equation provides the relationship between energy and probability. If we know how the free energy depends on some coordinate r , then the probability distribution for that coordinate is P(r) = e -G(r)/RT Equation 1 There are many cases where we do not know how the energy depends on a coordinate of interest, and we would like to determine it. In such cases, we can run a simulation and measure the probability distribution P(r) . We can then calculate an effective free energy, V(r) , by inverting equation 1: V(r) = -RT ln(P(r)) Equation 2 This effective free energy is called a potential of mean force (PMF) . Let us consider a specific case, where the coordinate of interest is the ethane torsion angle φ . The difference in PMF between two points, V( φ 2 ) – V( φ 1 ) , is equal to the reversible work done when ethane rotates from φ 1 to φ 2 , averaged over all degrees of freedom, i.e. , all values of bond lengths and bond angles. PMFs for bond stretching and bond angle bending Open the Excel workbook(s) you used for your bond and angle data from the longer MD simulation on ethane (Sim2). You will create two histograms of the data, one for a bond length (either H-C or C-C) and another for a bond angle (either H-C-H or H-C-C). You will then calculate the PMFs from the observed probability distributions.

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

### What students are saying

• As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

Kiran Temple University Fox School of Business ‘17, Course Hero Intern

• I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

Dana University of Pennsylvania ‘17, Course Hero Intern

• The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

Jill Tulane University ‘16, Course Hero Intern