Sk Jahiruddin

4 Questions 23 Answers 0 Followers

Questions related from Sk Jahiruddin

How do you simulate an unnatural base pair inside DNA?

I want to perform a molecular dynamics simulation for an unnatural base pair inside DNA. I have done the parameterization of individual base pairs, terminating the pair-sugar junction by methyl...

28 October 2014 2,031 6 View

How useful the CHARMM parameters generated by SWISSPARAM?

I want to perform a basic level of molecular dynamics with some unknown residue to check the stability of the molecule in 300K with aqueous environment. My study would be simple with no complex...

25 September 2014 9,060 11 View

Why do we divide the region of interest in different windows in ABF in NAMD?

While performing Adaptive Bias Force method free energy calculation in NAMD we divide our region of PMF (Potential of Mean Force) in different windows and then merge the .pmf files performing...

25 August 2014 7,428 3 View

How can I calculate the basis set superposition error in gaussian?

I'm optimizing DNA base pairs in gaussian. I have optimized base pairs individually and in pair both. Right now I want to find the basis set superposition error in those optimization.

13 August 2014 821 2 View