Hi all, I'm running an expanded ensemble simulation using gromacs 4.6.3 and it crashed with the error:
Fatal error: Something wrong in choosing new lambda state with a Gibbs move -- probably underflow in weight determination. Denominator is: 0 1.0000002384e+00 i dE numerator weights 0 -9.1451739502e+02 0.0000000000e+00 0.0000000000e+00 1 -9.0000128174e+02 0.0000000000e+00 0.0000000000e+00 2 -8.8548516846e+02 0.0000000000e+00 0.0000000000e+00 3 -8.7096899414e+02 0.0000000000e+00 0.0000000000e+00 4 -8.5645288086e+02 0.0000000000e+00 0.0000000000e+00 5 -8.4193676758e+02 0.0000000000e+00 0.0000000000e+00 6 -8.2742059326e+02 0.0000000000e+00 0.0000000000e+00 7 -8.1290447998e+02 0.0000000000e+00 0.0000000000e+00 8 -7.9838836670e+02 0.0000000000e+00 0.0000000000e+00 9 -7.8387219238e+02 0.0000000000e+00 0.0000000000e+00 10 -7.6935607910e+02 0.0000000000e+00 0.0000000000e+00 11 -7.5483990479e+02 0.0000000000e+00 0.0000000000e+00 12 -7.4032379150e+02 0.0000000000e+00 0.0000000000e+00 13 -7.2580767822e+02 0.0000000000e+00 0.0000000000e+00 14 -7.1129150391e+02 0.0000000000e+00 0.0000000000e+00 15 -6.9677539062e+02 0.0000000000e+00 0.0000000000e+00 16 -6.8225927734e+02 0.0000000000e+00 0.0000000000e+00 17 -6.6774316406e+02 0.0000000000e+00 0.0000000000e+00 18 -6.5322698975e+02 0.0000000000e+00 0.0000000000e+00 19 -6.3871087646e+02 0.0000000000e+00 0.0000000000e+00 20 -6.2419470215e+02 0.0000000000e+00 0.0000000000e+00 21 -6.0967858887e+02 0.0000000000e+00 0.0000000000e+00 22 -5.9516247559e+02 0.0000000000e+00 0.0000000000e+00 23 -5.8064630127e+02 0.0000000000e+00 0.0000000000e+00 24 -5.6613018799e+02 0.0000000000e+00 0.0000000000e+00 25 -5.5161407471e+02 0.0000000000e+00 0.0000000000e+00 26 -5.3709790039e+02 0.0000000000e+00 0.0000000000e+00 27 -5.2258178711e+02 0.0000000000e+00 0.0000000000e+00 28 -5.0806564331e+02 0.0000000000e+00 0.0000000000e+00 29 -4.9354953003e+02 0.0000000000e+00 0.0000000000e+00 30 -4.7903335571e+02 0.0000000000e+00 0.0000000000e+00 31 -4.6451724243e+02 0.0000000000e+00 0.0000000000e+00 32 -4.5000018311e+02 0.0000000000e+00 0.0000000000e+00 33 -4.3548400879e+02 0.0000000000e+00 0.0000000000e+00 34 -4.2096792603e+02 0.0000000000e+00 0.0000000000e+00 35 -4.0645178223e+02 0.0000000000e+00 0.0000000000e+00 36 -3.9193563843e+02 0.0000000000e+00 0.0000000000e+00 37 -3.8107025146e+02 0.0000000000e+00 0.0000000000e+00 38 -3.6290338135e+02 0.0000000000e+00 0.0000000000e+00 39 -3.4838723755e+02 0.0000000000e+00 0.0000000000e+00 40 -3.3387109375e+02 0.0000000000e+00 0.0000000000e+00 41 -3.1935494995e+02 0.0000000000e+00 0.0000000000e+00 42 -3.0483883667e+02 0.0000000000e+00 0.0000000000e+00 43 -2.9032269287e+02 0.0000000000e+00 0.0000000000e+00 44 -2.7580654907e+02 0.0000000000e+00 0.0000000000e+00 45 -2.6129040527e+02 0.0000000000e+00 0.0000000000e+00 46 -2.4677430725e+02 0.0000000000e+00 0.0000000000e+00 47 -2.3225816345e+02 0.0000000000e+00 0.0000000000e+00 48 -2.1774200439e+02 0.0000000000e+00 0.0000000000e+00 49 -2.0322586060e+02 0.0000000000e+00 0.0000000000e+00 50 -1.8970976257e+02 0.0000000000e+00-1.0000000000e+00 51 -1.7419361877e+02 0.0000000000e+00 0.0000000000e+00 52 -1.5967747498e+02 0.0000000000e+00 0.0000000000e+00 53 -1.4516131592e+02 0.0000000000e+00 0.0000000000e+00 54 -1.3064523315e+02 0.0000000000e+00 0.0000000000e+00 55 -1.1612908173e+02 0.0000000000e+00 0.0000000000e+00 56 -1.0161293030e+02 7.0064923216e-45 0.0000000000e+00 57 -8.7096786499e+01 1.4939846888e-38 0.0000000000e+00 58 -7.2580688477e+01 3.0102835162e-32 0.0000000000e+00 59 -5.8064540863e+01 6.0658294505e-26 0.0000000000e+00 60 -4.3548393250e+01 1.2222865341e-19 0.0000000000e+00 61 -2.9032243729e+01 2.4629560544e-13 0.0000000000e+00 62 -1.5516148567e+01 1.8256696421e-07-1.0000000000e+00 63 0.0000000000e+00 9.9999976158e-01-1.0000000000e+00 The mdp options for the free energy and expanded ensemble stuff are: free-energy = expanded ; no need to mess with these for now ;-------- sc-alpha = 0 sc-power = 0 sc-r-power = 6 sc-coul = no ------- ; Which intermediate state are we simulating? ------- init-lambda-state = 0 ; What are the values of lambda at the intermediate states? ;------- ; fep-lambdas = 0.0 0.06667 0.1333 0.2 0.2667 0.3333 0.4 0.4667 0.5333 0.6 0.6667 0.7333 0.8 0.8667 0.9333 1.0 bonded-lambdas = 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 vdw-lambdas = 0.000000 0.015873 0.031746 0.047619 0.063492 0.079365 0.095238 0.111111 0.126984 0.142857 0.158730 0.174603 0.190476 0.206349 0.222222 0.238095 0.253968 0.269841 0.285714 0.301587 0.317460 0.333333 0.349206 0.365079 0.380952 0.396825 0.412698 0.428571 0.444444 0.460317 0.476190 0.492063 0.507937 0.523810 0.539683 0.555556 0.571429 0.58331 0.603175 0.619048 0.634921 0.650794 0.666667 0.682540 0.698413 0.714286 0.730159 0.746032 0.761905 0.777778 0.793651 0.809524 0.825397 0.841270 0.857143 0.873016 0.888889 0.904762 0.920635 0.936508 0.952381 0.968254 0.984127 1.000000 mass-lambdas = 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 coul-lambdas = 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 restraint-lambdas = 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ; This makes sure we print out the differences in Hamiltonians between all states, and not just the neighboring states ;-------- calc-lambda-neighbors = -1 ; the frequency the free energy information is calculated. This ; frequency (every 0.2 ps) is pretty good for small molecule solvation. ;------- nstdhdl = 1000 ; not required, but useful if you are doing any temperature reweighting. Without ; temperature reweighting, you don't need the total energy -- differences are enough dhdl-print-energy = yes ; We are doing free energies with the LIPO_MUT molecule alone couple-moltype = LIPO_MUT ; we are mutating on type of molecule into another. In the initial state, both are on couple-lambda0 = vdw-q ; in the final state, both are on. couple-lambda1 = vdw-q ; let the intramolecular interaction be coupled too couple-intramol = yes ; expanded ensemble stuff nstexpanded = 100 ; Wang-Landau algorithm to determine the free energies 'weights' of the states lmc-stats = wang-landau ; Metropolized gibbs algorithm to move between states lmc-move = metropolized-gibbs ; we stop equilibrating when the wang-landau scaling term gets as low as 0.0001 lmc-seed = 7890 lmc-weights-equil = wl-delta weight-equil-wl-delta = 0.0001 ; Seed for Monte Carlo in lambda space ; We scale our wang landau weight by 0.7, whenever the smallest state ; and largest state have ratio of 0.8. The initial wang-landau weight ; increment delta is 1 kbT, and when this delta<1/N, where N is the ; number of attempted switches in state space, we use 1/N as the delta, ; which is less prone to saturation (stopping at the wrong value because ; the weight schedule lowered too quickly). wl-scale = 0.7 wl-ratio = 0.8 init-wl-delta = 1 ; this is 1*kB*T wl-oneovert = yes ; frequency to output transition matrix nst-transition-matrix = 10000000 Any idea? Thanks, Dejun -- 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
