rose,
please always reply to the mailing list, not individual people.
Thanks for your response. Unfortunately, i am not in the school and do not have an adviser or someone who can train me. I am trying to learn both MD and LAMMPS at the same time because I will do some calculations at work. I have been reading lots of things to understand the thermostating but seems like i could not get the idea yet.
that is my point. it is a very bad idea to try learning MD without
having somebody to advise and train you. while things may seem simple,
there are many, many practical details where it is necessary to talk
with somebody that has experience. doing good and dependable MD
simulations is as much a craft as it is science.
if you do not follow this advice, you are bound to repeat many
mistakes that many people have done before you because of lack of
experience. keep in mind that this is a field where there is a pool of
people with decades of experience.
axel.