[gmx-users] Can g_wham support using different temperature for different windows?

[chris.neale at utoronto.ca]

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