I made a model for my protein using Modeller with template having 46% identity. Now I want to use Gromacs for energy minimization and molecular dynamics simulation.
I see different simulation time (like; 200 ps, 1000ps, 5 ns,...) in papers. Does anyone have suggestions about the best time of simulation, and factors that affect the decision?
There is no easy answer for this question. The amount of time required for a simulation depends a lot upon the properties that you want to study, and how long the system will need to provide you with sufficiently high-quality data that your answers will be reliable. A time appropriate for one system may be completely insufficient or overkill for another simulation of a different material or under different state conditions.
There are a few basic rules of thumb that you can follow:
(1) You need to an equilibrate a system until there is no discernible trace of how you "built" the system in the data that you're collecting.
(2) Your "production runs" should be long enough to reduce the uncertainty in your your statistical averaging to an "acceptable" level. (You can specify what that level of uncertainty is. The uncertainty in the averaging can be predicted using classical tools, or can be estimated with methods such as those developed by Flyvbjerg and Petersen.)
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