Dear Amber Users,
I am performing a SMD for the reaction which involves simultaneous bond
break and bond tranfer steps. Here's the link for the reaction which I am
studying: https://drive.google.com/open?id=0B6ehLXK0eP7sX050M21kUmljNjQ.
I am confused about following points:
1. How to determine the number of SMD simulations to perform?
2. How to check for the convergence of the SMD simulation?
Moreover, how to set the sign of rstwt variable as -1 or +1? When should it
be positive and when it should be negative? In my case, I have selected
bond break as positive and proton/atom transfer as negative. Is this right
or wrong?
Any advice or suggestion would be highly appreciated.
Thanks in advance for help.
--
*Best Regards*
BM
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Received on Sun Aug 07 2016 - 23:00:02 PDT
