I read in Amber12 manual (Section 5.8.1, p.132)
leap recognizes water if the residue name is WAT or HOH. In later simulations, they may have to be tethered (more or less strongly) to their original positions to prevent them from "evaporating”.
I haven’t been able to find a way to tether WAT during long production MD simulations. Any ideas how to do so would be greatly appreciated.
Thanks in advance
George
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Received on Sat Oct 04 2014 - 13:00:02 PDT
