On Sun, Apr 20, 2014 at 9:47 AM, Nitin Sharma <sharmanitin.nus.edu.sg>wrote:
> Dear amber users,
>
> I have looked into many tutorials but I am confused regarding few things
>
> I know for before running molecular dynamics simulation
>
>
> 1) We need to solvate system
>
> 2) Add ions to make system neutral.
>
> 3) Minimize the water molecules and counter ions followed by
> minimizing entire system
>
>
> Before heating up the system and equilibrating with protein restraints
> and finally proceeding for MD
>
Why do you need to do each step you listed above? Another way of asking
this is "what effect does each step have and what potential artifacts or
problems does it help avoid"?
Do we need to perform steps 1 to 3 before simulated annealing too?
>
If you can answer the question I posed above, you should be able to
determine this yourself. You should also think about what simulated
annealing is and how it differs from MD at room temperature (for instance,
you need a shorter time step at high temperatures than you do at low
temperatures).
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Apr 20 2014 - 08:30:02 PDT
