Dear all,
I am trying to calculate PMF(potential of mean force) along a distance
using AMBER. I have done 97 simulations placing a particular molecule at 97
different points along the distance coordinate. The distance distributions
show considerable overlap as can be seen by the reaction.histogram which I
have attached. I am using Professor Grossfield's 'wham' program to
calculate the PMF.
The problem is, when PMF is calculated with the command
./wham 10.8 34.2 78 0.0001 300.0 1 metadatafile 97_20k.pmf >
97_20k.log
almost all the probability (0.860969) gets concentrated at 10.95.
#Coor Free +/- Prob +/-
10.650000 7.808876 -nan 0.000002 -nan
10.950000 0.000000 -nan 0.860969 -nan
11.250000 1.212829 -nan 0.112086 -nan
11.550000 2.240838 -nan 0.019909 -nan
11.850000 3.006684 -nan 0.005495 -nan
12.150000 3.936132 -nan 0.001152 -nan
12.450000 4.999682 -nan 0.000193 -nan
12.750000 5.516777 -nan 0.000081 -nan
13.050000 5.907733 -nan 0.000042 -nan
13.350000 7.185598 -nan 0.000005 -nan
13.650000 7.481728 -nan 0.000003 -nan
13.950000 7.616759 -nan 0.000002 -nan
14.250000 7.791042 -nan 0.000002 -nan
14.550000 7.257627 -nan 0.000004 -nan
14.850000 7.699594 -nan 0.000002 -nan
15.150000 8.394635 -nan 0.000001 -nan
15.450000 8.435193 -nan 0.000001 -nan
15.750000 8.319693 -nan 0.000001 -nan
16.050000 7.899175 -nan 0.000001 -nan
16.350000 7.520675 -nan 0.000003 -nan
16.650000 7.350089 -nan 0.000004 -nan
16.950000 7.144262 -nan 0.000005 -nan
17.250000 6.815532 -nan 0.000009 -nan
17.550000 6.926580 -nan 0.000008 -nan
17.850000 7.360287 -nan 0.000004 -nan
18.150000 7.322875 -nan 0.000004 -nan
18.450000 7.640881 -nan 0.000002 -nan
18.750000 8.092909 -nan 0.000001 -nan
19.050000 8.263583 -nan 0.000001 -nan
19.350000 8.647279 -nan 0.000000 -nan
19.650000 9.453315 -nan 0.000000 -nan
19.950000 9.621312 -nan 0.000000 -nan
20.250000 9.819468 -nan 0.000000 -nan
20.550000 9.990643 -nan 0.000000 -nan
20.850000 10.504337 -nan 0.000000 -nan
21.150000 10.727750 -nan 0.000000 -nan
21.450000 10.831247 -nan 0.000000 -nan
21.750000 10.968361 -nan 0.000000 -nan
22.050000 11.483583 -nan 0.000000 -nan
22.350000 11.713253 -nan 0.000000 -nan
22.650000 12.165046 -nan 0.000000 -nan
22.950000 12.440480 -nan 0.000000 -nan
23.250000 12.481515 -nan 0.000000 -nan
23.550000 12.357771 -nan 0.000000 -nan
23.850000 12.082079 -nan 0.000000 -nan
24.150000 11.797020 -nan 0.000000 -nan
24.450000 11.701011 -nan 0.000000 -nan
24.750000 11.550476 -nan 0.000000 -nan
25.050000 11.047749 -nan 0.000000 -nan
25.350000 10.919919 -nan 0.000000 -nan
25.650000 11.163292 -nan 0.000000 -nan
25.950000 11.053891 -nan 0.000000 -nan
26.250000 10.481810 -nan 0.000000 -nan
26.550000 10.423612 -nan 0.000000 -nan
26.850000 10.313436 -nan 0.000000 -nan
27.150000 10.132487 -nan 0.000000 -nan
27.450000 9.918259 -nan 0.000000 -nan
27.750000 9.663974 -nan 0.000000 -nan
28.050000 9.614350 -nan 0.000000 -nan
28.350000 9.817018 -nan 0.000000 -nan
28.650000 9.833279 -nan 0.000000 -nan
28.950000 9.848224 -nan 0.000000 -nan
29.250000 10.232477 -nan 0.000000 -nan
29.550000 10.054117 -nan 0.000000 -nan
29.850000 9.692431 -nan 0.000000 -nan
30.150000 9.123378 -nan 0.000000 -nan
30.450000 8.852411 -nan 0.000000 -nan
30.750000 8.441608 -nan 0.000001 -nan
31.050000 8.014642 -nan 0.000001 -nan
31.350000 7.693466 -nan 0.000002 -nan
31.650000 7.795882 -nan 0.000002 -nan
31.950000 8.136751 -nan 0.000001 -nan
32.250000 8.386743 -nan 0.000001 -nan
32.550000 8.583118 -nan 0.000000 -nan
32.850000 8.899569 -nan 0.000000 -nan
33.150000 8.909652 -nan 0.000000 -nan
33.450000 8.861119 -nan 0.000000 -nan
33.750000 8.516236 -nan 0.000001 -nan
34.050000 7.808876 -nan 0.000002 -nan
34.350000 0.000000 -nan 0.860969 -nan
#Window Free +/-
#0 0.000000 -nan
#1 0.558498 -nan
#2 1.130566 -nan
#3 1.756719 -nan
#4 2.698522 -nan
#5 3.090608 -nan
#6 3.397631 -nan
#7 4.138555 -nan
#8 4.492565 -nan
#9 4.955348 -nan
#10 5.170213 -nan
#11 5.258698 -nan
#12 5.255078 -nan
#13 5.055978 -nan
#14 4.957377 -nan
#15 5.323800 -nan
#16 5.710866 -nan
#17 5.962826 -nan
#18 5.976558 -nan
#19 5.768377 -nan
#20 5.506420 -nan
#21 5.261064 -nan
#22 5.010233 -nan
#23 4.811257 -nan
#24 4.638065 -nan
#25 4.471429 -nan
#26 4.504458 -nan
#27 4.682320 -nan
#28 4.877600 -nan
#29 4.931259 -nan
#30 5.149352 -nan
#31 5.395898 -nan
#32 5.741836 -nan
#33 6.007907 -nan
#34 6.290791 -nan
#35 6.925992 -nan
#36 7.159492 -nan
#37 7.354654 -nan
#38 7.481433 -nan
#39 7.771686 -nan
#40 8.057583 -nan
#41 8.306121 -nan
#42 8.392598 -nan
#43 8.539776 -nan
#44 8.751357 -nan
#45 9.152848 -nan
#46 9.347933 -nan
#47 9.738337 -nan
#48 9.938098 -nan
#49 10.036732 -nan
#50 9.932958 -nan
#51 9.683884 -nan
#52 9.505475 -nan
#53 9.370011 -nan
#54 9.287224 -nan
#55 9.184366 -nan
#56 8.969140 -nan
#57 8.703106 -nan
#58 8.574605 -nan
#59 8.561688 -nan
#60 8.663351 -nan
#61 8.658094 -nan
#62 8.439430 -nan
#63 8.153154 -nan
#64 8.007116 -nan
#65 7.943718 -nan
#66 7.849646 -nan
#67 7.727590 -nan
#68 7.592033 -nan
#69 7.514357 -nan
#70 7.361412 -nan
#71 7.292273 -nan
#72 7.229384 -nan
#73 7.242339 -nan
#74 7.341128 -nan
#75 7.401717 -nan
#76 7.415802 -nan
#77 7.499715 -nan
#78 7.676263 -nan
#79 7.624492 -nan
#80 7.253869 -nan
#81 6.916200 -nan
#82 6.544325 -nan
#83 6.312646 -nan
#84 5.902258 -nan
#85 5.633176 -nan
#86 5.347762 -nan
#87 5.336276 -nan
#88 5.432574 -nan
#89 5.626945 -nan
#90 5.820900 -nan
#91 5.980173 -nan
#92 6.126139 -nan
#93 6.295844 -nan
#94 6.444728 -nan
#95 6.473352 -nan
#96 6.409720 -nan
I have tried hard to understand what is going on but couldn't come up with
an explanation. If anyone could please give me some guidance to overcome
this issue I would be highly obliged.
Thank you very much
Sajeewa Dewage
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Received on Fri Dec 28 2012 - 06:30:03 PST
