Force Field Duration

[Former user]

When we calculate NMA for a protein and using default or user defined force field, how long time it is taking to perturbed the protein structure. For example, during the MM MD run we use 10ns, 20ns, 50ns etc.. Likewise what are the time periods for NMA run or how we have to calculate.

[Xinqiu Yao]

Hi,

NMA does not actually simulate the system, and so there is no concept of "time". What it provides is the information how the system can oscillate around the energy minimum. Or, in an energetic point of view, it gives the directions of motion associated with lowest energies.

Hope it can help.