Hello Chris, thanks for your attention. I'm sending you some links to some tests I performed. As I said you will notice that depending on the parameter used my simulation shows PMF profiles quite different. Especially what concerns to the difference between the use or not of the PBC.
https://sites.google.com/site/fileti/files/test1.jpg https://sites.google.com/site/fileti/files/test2.jpg https://sites.google.com/site/fileti/files/histo.png I have constructed two very similar topologies (ben-a.itp and ben-b.itp) where I put a virtual site in the center of benzene. This sites were restrained to keep my molecules fixed distance desired. The basic details of the simulations are given below:1000 define = -DPOSRES integrator = sd tinit = 0 dt = 0.002 nsteps = 5000000 or 500000 comm-mode = angular nstcomm = 1 comm-grps = System bd-fric = 1 ld-seed = 1993 nstlist = 5 ns_type = simple pbc = no or xyz periodic_molecules = no rlist = 0 coulombtype = Cut-off vdw-type = Cut-off rvdw = 0 DispCorr = no Tcoupl = Nose-Hoover tc_grps = system tau_t = 0.1 ref_t = 300 Pcoupl = no pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 constraints = all-bonds constraint_algorithm = lincs ; COM PULLING pull = umbrella pull_geometry = distance pull_dim = N N Y pull_r1 = 1 pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = BENa pull_weights0 = pull_pbcatom0 = 0 pull_group1 = BENb pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = 0 0 1 pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1700 or _______________________________________ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br > Dear Eudes: > > Can you please elaborate on your description? What .mdp options are > you using? What exactly do your curves look like (you can post > pictures to photobucket or some other online service and link them > here)? If you suspect that you are doing something wrong, then we need > to understand exactly what you are doing and exactly what you are > seeing in order to help. > > Chris. > > -- original message -- > > Hi gmx-users, > I'm trying to simulate a umbrella sampling PMF between two benzene > molecules > in vacuum. My protocol is working fine, my histograms have good overlap and > the curves I have got are quite reasonable. > > However I have noticed that some options in my .mdp file can significantly > change > the depth of the well. Also the curves can not go to zero at long > distances. > For example, if I use PBC I get a reasonably good value for the minimum of > the PMF > but from a certain separation it starts to increase slightly in a linear > fashion > instead of going to zero. On the other hand, if I make pbc = no, I get an > acceptable curve, > with the PMF going to zero, but with the minimum too high. > > Someone could give me any tips on the best set of parameters to calculate > this PMF in a vacuum? > bests > eef > > >
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