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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
