Sounds like unconverged sampling. You would be astounded how long
systems like this can take to converge. An all-atom simulation like
this can easily require >10 us (microseconds!) per umbrella. I don't
know about martini, probably a lot less.
Chris.
-- original message --
Thanks Justin.
I tried your suggestions by either increase more windows and change the force
constant, but it seems the samplings are still bad in some windows. When I did
pulling in (0 0 1) direction and a reverse pulling in (0 0 -1)
direction, I got
different configurations at certain reaction coordinates. And the windowed
umbrella sampling seems depends strongly on the initial configurations in that
window. Therefore I got different PMFs using pulling in (0 0 1) direction and
reverse pulling in ?0 0 -1) direction.
In my simulation, I exert constraints on phosphate atoms in z direction, so
there is no lipid flip-flop and the membrane will be stable at high
temperatures. Then I am thinking of increasing temperature in those
bad windows
to enhance sampling...
best regards,
Jianguo
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