Azadeh Alavizargar

2 Questions 3 Answers 0 Followers

Questions related from Azadeh Alavizargar

Should we use the features in productions runs of membrane-protein simulations in the SMD or ABF simulations?

I wish to know if we should keep some features of production runs of membrane-protein simulations such as useFlexibleCell or useConstantArea or wrapAll for SMD or ABF simulations, or we just use...

23 October 2014 6,416 2 View

How important is the position of ion in each window in ABF simulations?

I need to know whether the exact initial position of ion within each window to calculate the free energy via the ABF method is important, and what would be the best position for this purpose? Thanks.

17 September 2014 9,444 3 View