[gmx-users] Umberella sampling

[chris.neale at utoronto.ca]

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
afew question in umberella sampling tutorial:
1-We do umberella sampling for each of 25 simulation windows,while using a
spring(harmonic potential),Are these springs 1 or 3 dimensional?

2-Suppose the length of one windows is X nm,what is the  approperiate K
(spring constant) for this window?Is there a general way to determine this
value?

3-I think the K must be such that the oscilation amplitude be  a few larger
than X/2, because we need overlapping of density distribution for analysing
with wham method, am I right?

Thanks in advance