Mohsen:
To be honest, this just sounds like debating. I have offered you my
perspective already.
Chris.
-- original message --
Dear chris
Thanks for your reply
1-I am not sure,Since we need the know the variations of free energy along a
specific degree of freedom of system(for example z axis),so the springs
must be 1 dimensional to allow drug to oscilate only in one dimension(z
axis).
Let me say my question in other words:
Do we need to do sampling just in phase space related to z axis(1
dimensional) or we can do sampling in other places(if it be 3
dimensional),Although we still want the variation of free energy along z
axis?
2-evry windows have a width(for example 0.02 nm),Besides according to Hock's
law knowing the oscilation amplitude is possible when you have the K and the
mass and total energy:1/2 k(x/2)^2=1/2 m v(max)^2
3-my question in other words:
Since we need overlapping the distribution densities of each windows,Does
the drug need to enter to the neighbour windows a little ?
Thanks in advance for your reply
On Tue, Mar 15, 2011 at 9:54 AM, <chris.neale at utoronto.ca> wrote:
1. Depends on how you set them in your .mdp file. It could be either.
2. There is no general method. Use trial and error. Also, your question is
flawed, K defines X. Unless by "length of one windows" you meant the
distance between neighbouring centers of restraint (umbrellas).
3. you need overlapping distributions. Let's leave it at that. I have not
seen any general treatment of what K is required and I am rather sure that
it is impossible to predetermine the necessary force constants (K) unless
you know the PMF. If you need to know the PMF beforehand then this is not a
general solution and also probably useless since the whole purpose is to get
the PMF.
Chris.
-- original message --
Dear All
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