Using a flexible reference to generate a PMF is certainly not a good
idea.
More than affecting your convergence, your distance may have only little
to do with the actual position of your ion in the channel. Imagine the
ion is
in a stable position and has to go over some energy barrier. It likely
that the
loop will move instead of your ion ...
You might want to change your the reaction coordinate.
On May 10, 2010, at 3:27 PM, chris.ne...@utoronto.ca wrote:
Dear Aswathy:
While not technically incorrect, it will make convergence much more
difficult and is probably realistically incorrect given today's cpu
power. But then again perhaps you have some particularly important
reason to make that choice. In the absence of that, find some
atom(s) that are as static as possible.
Chris.
-- original message --
Ok . Now I understood. I have one more doubt , as I mentioned to
you, I am
using one residue in the extracellular loop as a reference point.
Since this
is in the loop, do you think it can be good reference point (due to
th large
fluctuatuion in the loop, will it affect the result)?
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