[gmx-users] Umberella sampling

[chris.neale at utoronto.ca]

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