The most important is that you have to put in trajectories that
are equilibrated! You can mix as much force constant values
you like but always equilibrated ...
Then the lower the force constant the longer the simulation needs
to be to reach equilibrium: larger conformational space accessible.
I can also imagine that a too strong force constant might deform
your molecules in a manner you should not.
Then does it matter how many times you vary it, and how large ?
In my
sampling I have very good histograms up to 2 nm (force constant = 1000
kj/mol), above 2nm they are not. I feel I may have to use a force
constant of 500 for the next 3 or 4 windows, and even less again
(ca~ 50
kj/mol) beyond that.
Cheers
Gavin
XAvier Periole wrote:
On Aug 20, 2010, at 5:12 PM, Gavin Melaugh wrote:
Hi all
Is is O.K to use different force constants for different sampling
windows for the generation of the potential of mean force curves?
Yes.
Many Thanks
Gavin
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