Dear Amber users,
I need to simulate a two-domain protein. The two domains are expected to
separate during the MD. How should I select the solvation distance when
creating a box? I.e., the box should accommodate a two-domain protein which
becomes longer when the domains separate during the MD.
My understanding is that the protein in the cell #1 must not approach the
protein in the cell #2 closer than the specified by the 'cut' parameter
(the close range electrostatics). Therefore, if, e.g., I have used the 'at
least 25A' solvation distance and after the simulation I put the two cells
together in PyMol and the two proteins are at least 'cut' A away from each
other - than its OK. Am I right?
Thanks.
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Received on Mon Jul 03 2017 - 12:00:03 PDT
