[gmx-users] Question about g_bar output
Warren Gallin
wgallin at ualberta.ca
Wed Jun 29 20:16:34 CEST 2011
Hi,
I've just run g_bar on data from a simulation, and I am having trouble reconciling the graphical output with the numerical output. The units seem to be inconsistent.
In particular the numbers under detailed results are in units of kT, followed by final results in kJ/mole (see below).
However, the graphical output from -o and -oi seem to numerically be from the kT units list, but the y-axis is labelled in kJ/mole (see atached PDF files.
Am I missing something here, or is this a bug in the output code?
Warren Gallin
md_0.05.xvg: 0.0 - 2000.0; lambda = 0.050
foreign lambdas: 0.050 (100001 pts) 0.000 (100001 pts) 0.100 (100001 pts)
md_0.1.xvg: 0.0 - 2000.0; lambda = 0.100
foreign lambdas: 0.100 (100001 pts) 0.050 (100001 pts) 0.150 (100001 pts)
md_0.15.xvg: 0.0 - 2000.0; lambda = 0.150
foreign lambdas: 0.150 (100001 pts) 0.100 (100001 pts) 0.200 (100001 pts)
md_0.2.xvg: 0.0 - 2000.0; lambda = 0.200
foreign lambdas: 0.200 (100001 pts) 0.150 (100001 pts) 0.250 (100001 pts)
md_0.25.xvg: 0.0 - 2000.0; lambda = 0.250
foreign lambdas: 0.250 (100001 pts) 0.200 (100001 pts) 0.300 (100001 pts)
md_0.3.xvg: 0.0 - 2000.0; lambda = 0.300
foreign lambdas: 0.300 (100001 pts) 0.250 (100001 pts) 0.350 (100001 pts)
md_0.35.xvg: 0.0 - 2000.0; lambda = 0.350
foreign lambdas: 0.350 (100001 pts) 0.300 (100001 pts) 0.400 (100001 pts)
md_0.4.xvg: 0.0 - 2000.0; lambda = 0.400
foreign lambdas: 0.400 (100001 pts) 0.350 (100001 pts) 0.450 (100001 pts)
md_0.45.xvg: 0.0 - 2000.0; lambda = 0.450
foreign lambdas: 0.450 (100001 pts) 0.400 (100001 pts) 0.500 (100001 pts)
md_0.5.xvg: 0.0 - 2000.0; lambda = 0.500
foreign lambdas: 0.500 (100001 pts) 0.450 (100001 pts) 0.550 (100001 pts)
md_0.55.xvg: 0.0 - 2000.0; lambda = 0.550
foreign lambdas: 0.550 (100001 pts) 0.500 (100001 pts) 0.600 (100001 pts)
md_0.6.xvg: 0.0 - 2000.0; lambda = 0.600
foreign lambdas: 0.600 (100001 pts) 0.550 (100001 pts) 0.650 (100001 pts)
md_0.65.xvg: 0.0 - 2000.0; lambda = 0.650
foreign lambdas: 0.650 (100001 pts) 0.600 (100001 pts) 0.700 (100001 pts)
md_0.7.xvg: 0.0 - 2000.0; lambda = 0.700
foreign lambdas: 0.700 (100001 pts) 0.650 (100001 pts) 0.750 (100001 pts)
md_0.75.xvg: 0.0 - 2000.0; lambda = 0.750
foreign lambdas: 0.750 (100001 pts) 0.700 (100001 pts) 0.800 (100001 pts)
md_0.8.xvg: 0.0 - 2000.0; lambda = 0.800
foreign lambdas: 0.800 (100001 pts) 0.750 (100001 pts) 0.850 (100001 pts)
md_0.85.xvg: 0.0 - 2000.0; lambda = 0.850
foreign lambdas: 0.850 (100001 pts) 0.800 (100001 pts) 0.900 (100001 pts)
md_0.9.xvg: 0.0 - 2000.0; lambda = 0.900
foreign lambdas: 0.900 (100001 pts) 0.850 (100001 pts) 0.950 (100001 pts)
md_0.95.xvg: 0.0 - 2000.0; lambda = 0.950
foreign lambdas: 0.950 (100001 pts) 0.900 (100001 pts) 1.000 (100001 pts)
md_0.xvg: 0.0 - 2000.0; lambda = 0.000
foreign lambdas: 0.000 (100001 pts) 0.050 (100001 pts)
md_1.xvg: 0.0 - 2000.0; lambda = 1.000
foreign lambdas: 1.000 (100001 pts) 0.950 (100001 pts)
Writing histogram to histogram.xvg
Temperature: 300 K
Detailed results in kT (see help for explanation):
lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/-
0.000 0.050 -1.47 0.39 7.65 0.72 8.37 0.64 7.31 1.41
0.050 0.100 -1.34 0.27 7.53 0.48 7.30 0.14 5.98 0.42
0.100 0.150 -0.65 0.26 8.04 0.27 7.71 0.25 7.15 0.36
0.150 0.200 -0.30 0.44 7.98 0.27 8.13 0.20 7.55 0.30
0.200 0.250 -1.01 0.36 8.61 0.27 8.50 0.18 8.56 0.36
0.250 0.300 -0.47 0.19 6.99 0.21 7.48 0.26 6.26 0.31
0.300 0.350 -0.22 0.24 8.31 0.20 8.43 0.22 7.93 0.22
0.350 0.400 0.05 0.44 7.34 0.30 7.87 0.14 6.66 0.40
0.400 0.450 0.19 0.18 8.03 0.38 7.94 0.17 7.16 0.46
0.450 0.500 -0.11 0.11 8.40 0.16 8.34 0.20 7.99 0.26
0.500 0.550 -0.14 0.09 7.73 0.13 7.77 0.19 7.04 0.18
0.550 0.600 -0.05 0.29 8.18 0.15 8.06 0.27 7.51 0.17
0.600 0.650 -0.03 0.16 7.95 0.15 8.05 0.10 7.31 0.17
0.650 0.700 0.42 0.21 7.54 0.22 7.53 0.13 6.70 0.23
0.700 0.750 0.85 0.37 8.07 0.10 8.36 0.21 7.60 0.11
0.750 0.800 0.85 0.13 7.67 0.32 7.78 0.30 6.86 0.51
0.800 0.850 0.80 0.20 8.30 0.28 8.05 0.18 7.63 0.35
0.850 0.900 0.78 0.28 8.00 0.14 7.87 0.15 7.44 0.31
0.900 0.950 1.09 0.41 7.86 0.48 8.16 0.32 7.60 0.62
0.950 1.000 1.09 0.39 7.87 0.31 7.40 0.42 7.09 0.74
Final results in kJ/mol:
lambda 0.000 - 0.050, DG -3.67 +/- 0.98
lambda 0.050 - 0.100, DG -3.34 +/- 0.68
lambda 0.100 - 0.150, DG -1.62 +/- 0.64
lambda 0.150 - 0.200, DG -0.76 +/- 1.09
lambda 0.200 - 0.250, DG -2.52 +/- 0.90
lambda 0.250 - 0.300, DG -1.16 +/- 0.48
lambda 0.300 - 0.350, DG -0.55 +/- 0.60
lambda 0.350 - 0.400, DG 0.12 +/- 1.09
lambda 0.400 - 0.450, DG 0.47 +/- 0.44
lambda 0.450 - 0.500, DG -0.28 +/- 0.27
lambda 0.500 - 0.550, DG -0.36 +/- 0.21
lambda 0.550 - 0.600, DG -0.13 +/- 0.72
lambda 0.600 - 0.650, DG -0.06 +/- 0.39
lambda 0.650 - 0.700, DG 1.05 +/- 0.51
lambda 0.700 - 0.750, DG 2.12 +/- 0.93
lambda 0.750 - 0.800, DG 2.13 +/- 0.32
lambda 0.800 - 0.850, DG 2.01 +/- 0.50
lambda 0.850 - 0.900, DG 1.96 +/- 0.69
lambda 0.900 - 0.950, DG 2.72 +/- 1.02
lambda 0.950 - 1.000, DG 2.71 +/- 0.97
total 0.000 - 1.000, DG 0.85 +/- 2.91
-------------- next part --------------
A non-text attachment was scrubbed...
Name: bar.pdf
Type: application/pdf
Size: 4950 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110629/700a2037/attachment.pdf>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: barint.pdf
Type: application/pdf
Size: 4472 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110629/700a2037/attachment-0001.pdf>
More information about the gromacs.org_gmx-users
mailing list