Hello Amber users,
This is my first time, whenI do MD. So, my questions could seem so basic.
I have system ( two molecules ) in gas phase in periodic box. I want add pseudo-atom inside the big one molecule, which contains 150 atoms. Then put the considers between pseudo-atom and small molecule, 39 atoms. Additionally, I want determine, that four atoms of big molecules will be during the simulations at the same coordinates (don't move)-it's necessary, because my idea is observe how the small molecules go inside to the big particle.
Now, I have questions:
-when I must add pseudo-atom? during parametrizing in xleap? -what command?
- how can I cause the atoms in big molecule be in this same place during MD? (Do I must write script orin files add notes?)
Thank you in advance,
Anne Kichler
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Received on Thu Feb 07 2013 - 03:30:03 PST
