Jae Young Lee

5 Questions 5 Answers 0 Followers

Questions related from Jae Young Lee

Do I use the option of NAMD: harmonic restraint?

Hi~ I'm a graduate student studying MD simulation. When they use SMD simulation, many researchers used the option: harmonic restraint. Why do they use the option? What does it mean?

01 January 2017 4,127 8 View

What is the issue in Finite Elemet Method?

I am curious about FEM. What is the recent issue, difficult problem, or challengeable item in FEM? I heard that most issues of FEM have been solved.. But I think something difficult still remains...

10 October 2016 5,489 0 View

How can I formulate thee-dimensional plain-stress element ?

Hi everyone. when we formulate a finite element for plain-strain/stress, many books employ two-dimensional coordinate. But, for three-dimensional coordinate, how can we formulate a plain-stress...

09 September 2016 3,754 0 View

What is the unit and meaning of the eigenvalue in NMWiz of VMD (ProDy) ?

Hello. I am now focusing on finding natrual frequencies of biomolecules using NMWiz in VMD In VMD TkConsole, the function 'prody eda' can yield the eigenvalues using PDB and DCD...

08 August 2015 1,043 0 View

How can I set the PME gridsize when using "WrapWater on" and "WrapAll off" in NAMD?

HI, I have a quation to set a configuration file in NAMD (MD simulation) There was a problem when using an option, "WrapAll on" since a chain of DNA (target molecule) sometimes suddenly moved from...

02 February 2015 8,978 10 View