Dear Amber developers and users,
I am interested in doing MD simulation for a GC-rich ssRNA fragment, which have several internal H-bonds between base pairs. I did MD simulation by following the tutorial 1 in the Amber website. But, at the end of the simulation (with Na+ and explicit solvent), the internal H-bonds are separated.
My question is
How to hold H-bonds of base pairs fixed, and perform MD simulation for the rest atoms?
Thank you for your time.
Wu
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Received on Mon May 30 2011 - 18:30:02 PDT
