The appropriate time for an MD simulation depends on the size and complexity of the protein and the goal of the study:

Smaller proteins (

The simulation time depends on:

Dear Uddipta Ghosh Dastidar,

Residue number in a protein doesn't influence timeframe of simulation however, larger the protein it takes more time to complete the defined time frame. About the nature of protein, you prepare your unit cell environment according to the nature of protein.

Coming to time frames, depending on your requirement you will fix the time frame. to observe changes in bond angles, bond stretching femto to pico second simulation is sufficient. A nano second simulation helps you identify loop motion and hinge bending mostly concerned with ligand binding. To understand protein folding you need to go for micro, milli and seconds simulations.

Hope this helps.