[gmx-users] Expanded ensemble simulation died with fatal error: Something wrong in choosing new lambda state with a Gibbs move
Dejun Lin
dejun.lin at gmail.com
Wed Jul 31 20:15:18 CEST 2013
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
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