Dear all, I encountered problems when trying to keep a simple system at constant temperature, and would appreciate any help/advice!
I try to calculate a PMF between two relatively simple particles (about spherical, each 60 atoms) in solution with umbrella sampling. For now i model the solvent as primitive model electrolyte (vacuum + epsilonr=80), and what i see is this: trying out the following thermostats: * leapfrog + nose hoover * velocity verlet + 10 nose hoover chains * v-rescale in ALL cases, i get what seems to be a non-canonical distribution: Since the distance between the two particles is restrained via a harmonic potential one would expect (at least for large distances) to get an approximately Gaussian distribution of the distance between the two particles, centred near the equilibrium distance of the harmonic restraint. However, I keep seeing a bi-modal distribution (as one would expect from a harmonic oscillator with no thermostat) which, I believe, can be taken as evidence for a non-canonical phase space coverage (and probably this also screws up the WHAM analysis) My system is relatively simple - pathologically so one might argue - but then, what I recall from articles I read, especially about Nose Hoover chains, it seems that I could expect getting a proper canonical distribution even for much simpler systems with no more than a few degrees of freedom (and my system has >300 degrees of freedom) With Langevin dynamics (instead of md) the distance distribution DOES become Gaussian, but now I encounter a different problem: More so than with MD convergence becomes an issue: especially with small tau_t (<5 ps). E.g. to cover a distance of about 3 nm it takes at least 44 windows with >=1 ns each to get a reasonably converged PMF. So I wonder: i) is there any limit to the size of tau_t I am supposed to use? or ii) is there any other way to accelerate convergence? FTR: I also tried using two tc_grps (one for each particle) but, at least qualitatively, i see the same results. thanks in advance for any help! regards, Michael === mdp-file: integrator = sd ; or md, or md-vv-avek tau_t = 0.2 0.2 ; varies from 0.2 to 10.0 for sd ref_t = 300 300 tc_grps = p1 p2 ; or just System dt = 0.001 tinit = 0 nsteps = 400000 ; or more nstxtcout = 0 nstxout = 1000 nstvout = 0 nstfout = 0 nstenergy = 100 constraints = h-bonds comm_mode = Linear nstcomm = 1 pbc = no nstlist = 0 ns_type = simple rlist = 5.0 rcoulomb = 5.0 rvdw = 5.0 coulombtype = Cut-off vdwtype = User ; repulsive only LJ pot epsilon_r = 80 pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = p1 pull_group1 = p2 pull_rate1 = 0.0 pull_k1 = kkk ; varies from 500-5000 pull_nstxout = 100 pull_nstfout = 100 pull_pbcatom0 = 61 pull_pbcatom1 = 122 pull_init1 = ddd ; varies from 1-4 freezegrps = c1 c2 freezedim = Y Y N Y Y N ; this is to keep the particles in 1-D energygrps = p1 p2 -- 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