Hi,
I'm new to umbrella sampling and need to understand what I'm doing wrong. I've done a couple short runs in SANDER, then applied WHAM-2D to the results. SANDER seems to do the US okay, but WHAM-2D gives me NAN's and inf's.
If anyone could tell me where I'm going astray, I'd be very grateful.
Tom Allen
[Here is the SANDER input:]
Constant pressure and volume
&cntrl
nstlim=5000, dt=0.002, ntx=7, irest=1, ntpr=10, ntwr=50,ntwx=100,
temp0=300.0, ntt=1, tautp=2.0, taup=2.0,
ntb=2, ntp=1, iwrap=1,
ntc=2, ntf=2,
scee=1.2,cut=9.0,ig=82223,
nmropt=1,
/
&ewald
a=64.7200,b=51.4485,c=47.2283,alpha=90.0,beta=90.0,gamma=90.0,
/
&wt type='DUMPFREQ', istep1=5 /
&wt type='END' /
DISANG=chi.RST
DUMPAVE=chi45chi150
/
[And here is chi.RST:]
# torsion restraint for chi2, chi1
&rst iat=920,922,925,926, r1=-135.0, r2=45.0, r3=45.0, r4=225.0,
rk2=30.0. rk3=30.0, /
&rst iat=940,920,922,925, r1=-30.0, r2=150.0, r3=150.0, r4=330.0,
rk2=30.0. rk3=30.0, /
[This gives output like:]
0 44.877 153.367
5 86.618 141.604
10 109.211 140.343
15 110.702 137.209
20 113.208 143.991
25 105.173 145.803
30 106.859 147.284
35 117.856 141.634
40 116.685 137.146
45 119.050 138.211
50 117.336 139.854
55 111.523 134.821
60 109.094 131.449
65 111.331 137.381
70 107.103 135.835
75 113.673 136.010
80 118.471 133.802
85 112.863 133.295
90 134.540 133.677
95 144.482 132.683
100 136.580 132.286
.
.
.
[I use this metafile for WHAM-2D:]
# metafile for WHAM-2D
/Users/camdl/allen/chichi150 150 150 60.0 60.0
/Users/camdl/allen/chichi140150 140 150 60.0 60.0
[60.0 because of the 1/2 factor in the umbrella potential formalism. I get results like this:
# ./wham-2d Px 135 155 8 Py 145 155 8 0.01 300 0 meta.fkbp pmf2d.out
#Turning on periodicity in x with period = 360.000000
#Turning on periodicity in y with period = 360.000000
#Number of windows = 2
# Dumping simulation biases, in the metadata file order
# Window F (free energy units)
# 0 nan
# 1 nan
[silvergene2:~/allen/wham/wham-2d] camdl% more pmf2d.out
136.250000 145.625000 nan 0.000000 nan 0.000000
136.250000 146.875000 nan 0.000000 nan 0.000000
136.250000 148.125000 nan 0.000000 nan 0.000000
136.250000 149.375000 nan 0.000000 nan 0.000000
136.250000 150.625000 nan 0.000000 nan 0.000000
136.250000 151.875000 nan 0.000000 nan 0.000000
136.250000 153.125000 nan 0.000000 nan 0.000000
136.250000 154.375000 nan 0.000000 nan 0.000000
138.750000 145.625000 nan 0.000000 nan 0.000000
138.750000 146.875000 inf 0.000000 nan 0.000000
138.750000 148.125000 inf 0.000000 nan 0.000000
138.750000 149.375000 inf 0.000000 nan 0.000000
138.750000 150.625000 inf 0.000000 nan 0.000000
138.750000 151.875000 inf 0.000000 nan 0.000000
138.750000 153.125000 inf 0.000000 nan 0.000000
138.750000 154.375000 nan 0.000000 nan 0.000000
141.250000 145.625000 nan 0.000000 nan 0.000000
141.250000 146.875000 inf 0.000000 nan 0.000000
141.250000 148.125000 inf 0.000000 nan 0.000000
141.250000 149.375000 inf 0.000000 nan 0.000000
141.250000 150.625000 inf 0.000000 nan 0.000000
.
.
.
[So clearly I'm doing something wrong. When I lower the spring constants to 1.0 in WHAM-2D, I get output like this:]
# ./wham-2d Px 135 155 8 Py 145 155 8 0.01 300 0 meta.fkbp pmf2d.out
#Turning on periodicity in x with period = 360.000000
#Turning on periodicity in y with period = 360.000000
#Number of windows = 2
#Iteration 10: 4.109225
#Iteration 20: 0.091030
#Iteration 30: 0.091017
#Iteration 40: 0.090757
#Iteration 50: 0.086492
#Iteration 60: 0.070477
#Iteration 70: 0.051377
#Iteration 80: 0.031206
#Iteration 90: 0.005207
# Dumping simulation biases, in the metadata file order
# Window F (free energy units)
# 0 -0.019626
# 1 -83.815732
[silvergene2:~/allen/wham/wham-2d] camdl% more pmf2d.out
136.250000 145.625000 0.000000 0.000000 0.783365 0.000000
136.250000 146.875000 4.592876 0.000000 0.000347 0.000000
136.250000 148.125000 7.753940 0.000000 0.000002 0.000000
136.250000 149.375000 9.280376 0.000000 0.000000 0.000000
136.250000 150.625000 9.463292 0.000000 0.000000 0.000000
136.250000 151.875000 7.925076 0.000000 0.000001 0.000000
136.250000 153.125000 4.971211 0.000000 0.000184 0.000000
136.250000 154.375000 0.766115 0.000000 0.216101 0.000000
138.750000 145.625000 28.114020 0.000000 0.000000 0.000000
138.750000 146.875000 32.862068 0.000000 0.000000 0.000000
138.750000 148.125000 35.745866 0.000000 0.000000 0.000000
138.750000 149.375000 37.400067 0.000000 0.000000 0.000000
138.750000 150.625000 37.571202 0.000000 0.000000 0.000000
138.750000 151.875000 36.104087 0.000000 0.000000 0.000000
138.750000 153.125000 33.233363 0.000000 0.000000 0.000000
138.750000 154.375000 28.919808 0.000000 0.000000 0.000000
141.250000 145.625000 53.218653 0.000000 0.000000 0.000000
141.250000 146.875000 57.729325 0.000000 0.000000 0.000000
141.250000 148.125000 61.031153 0.000000 0.000000 0.000000
141.250000 149.375000 62.666587 0.000000 0.000000 0.000000
141.250000 150.625000 62.749728 0.000000 0.000000 0.000000
[Which looks a little better, but is not justified.]
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Received on Wed Nov 07 2007 - 06:07:29 PST
