Lulu Ning

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Questions related from Lulu Ning

How to handle the periodic condition problems in membrane simulation?

I have carried out MD simulations about membrane channel. In the process of MD simulations, the upper leaflet and the lower leaflet were separated as shown in figure 1. I tried to center the two...

10 October 2016 8,913 3 View

How to describe the mutants of a peptide in English?

when I write my new paper, I am really confused by the description of the mutants. For example, when I tried to describe PrP106-126 A116S, is "A116S mutated PrP106-126" right? or the A116S...

06 June 2014 8,633 0 View

How can I extract trajectories of more than 200 ns from replica exchange molecular dynamics simulations by amber?

When I finished REMD by amber 10 package, I tried to extract temperature trajectories. However, I can not extract the trajectory more than 200 ns even 300 replica exchange molecular dynamics...

03 March 2014 5,511 2 View

How can you explain the relation between a residue-residue backbone hydrogen bond and the secondary structure of a protein?

When I tried to analyse the structural diversity of a peptide and its mutants, I found it is difficult to connect the probability of hydrogen bond formation of a residue with its propensity to...

02 February 2014 6,672 3 View

Does minor charge of ligand affect the results of molecular dynamics simulations?

When I tried to construct the force field of a ligand, the resulting charge of the molecule is -0.000004, not zero. How does the minor charge affect the dynamics of its acceptor?

12 December 2013 5,626 0 View