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.ne...@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 > 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 > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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