[gmx-users] Umberella sampling
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Tue Mar 15 17:54:28 CET 2011
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
More information about the gromacs.org_gmx-users
mailing list