Please keep the discussion on the list; I'm not a private tutor.
Saeid Akbarshahi wrote:
Dear Justin
I have simulated this system with this structure and files.Could you
tell me, is my structure correct?
I have no clue what is in your system, what settings were used for the
simulation, or anything else so I cannot make any assessment whatsoever.
I am a novice user.
It is in your best interest to do lots of homework before running a simulation
and hoping it's right. Ask yourself: what protocols have others used? What
have they analyzed? Why have they done these things? Unless you can answer all
of these questions and understand the logic behind the choices made, you're not
ready to do simulations if you rely on keeping your fingers crossed, hoping to
have someone check your work for you. There is a steep learning curve for doing
MD simulations properly, but doing the proper preparation now will save you tons
of time (and wasted data) later on.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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