I install amber today. Fist I install amber with out the bugfix.all and all
test pass. then I apply the bugfix.all a run the test and the pb_pgb test
fail. This is the output:
66c66
< Etot = -14371.5201 EKtot = 3870.9870 EPtot =
-18242.5071
---
> Etot = -14329.6226 EKtot = 3870.9870 EPtot =
-18200.6096
69c69,70
< EELEC = -24281.4685 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24281.4685 EGB = 0.0000 RESTRAINT =
41.8975
> EAMBER (non-restraint) = -18242.5071
72c73
< Etot = -14371.3557 EKtot = 3855.1841 EPtot =
-18226.5398
---
> Etot = -14329.7248 EKtot = 3855.1841 EPtot =
-18184.9089
75c76,77
< EELEC = -24277.4299 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24277.4299 EGB = 0.0000 RESTRAINT =
41.6310
> EAMBER (non-restraint) = -18226.5398
78c80
< Etot = -14371.0657 EKtot = 3845.7886 EPtot =
-18216.8542
---
> Etot = -14329.6623 EKtot = 3845.7886 EPtot =
-18175.4508
81c83,84
< EELEC = -24274.7240 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24274.7240 EGB = 0.0000 RESTRAINT =
41.4034
> EAMBER (non-restraint) = -18216.8542
84c87
< Etot = -14371.2605 EKtot = 3843.8455 EPtot =
-18215.1060
---
> Etot = -14330.0477 EKtot = 3843.8455 EPtot =
-18173.8933
87c90,91
< EELEC = -24273.3960 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24273.3960 EGB = 0.0000 RESTRAINT =
41.2128
> EAMBER (non-restraint) = -18215.1060
90c94
< Etot = -14371.3474 EKtot = 3848.9511 EPtot =
-18220.2985
---
> Etot = -14330.2871 EKtot = 3848.9511 EPtot =
-18179.2382
93c97,98
< EELEC = -24272.3671 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24272.3671 EGB = 0.0000 RESTRAINT =
41.0603
> EAMBER (non-restraint) = -18220.2985
96c101
< Etot = -14371.4557 EKtot = 3859.3314 EPtot =
-18230.7872
---
> Etot = -14330.5031 EKtot = 3859.3314 EPtot =
-18189.8346
99c104,105
< EELEC = -24271.6192 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24271.6192 EGB = 0.0000 RESTRAINT =
40.9526
> EAMBER (non-restraint) = -18230.7872
acruz.tccg8:~/amber8/test/pb_pgb> cat mdout.pbpgb.dif
66c66
< Etot = -14371.5201 EKtot = 3870.9870 EPtot =
-18242.5071
---
> Etot = -14329.6226 EKtot = 3870.9870 EPtot =
-18200.6096
69c69,70
< EELEC = -24281.4685 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24281.4685 EGB = 0.0000 RESTRAINT =
41.8975
> EAMBER (non-restraint) = -18242.5071
72c73
< Etot = -14371.3557 EKtot = 3855.1841 EPtot =
-18226.5398
---
> Etot = -14329.7248 EKtot = 3855.1841 EPtot =
-18184.9089
75c76,77
< EELEC = -24277.4299 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24277.4299 EGB = 0.0000 RESTRAINT =
41.6310
> EAMBER (non-restraint) = -18226.5398
78c80
< Etot = -14371.0657 EKtot = 3845.7886 EPtot =
-18216.8542
---
> Etot = -14329.6623 EKtot = 3845.7886 EPtot =
-18175.4508
81c83,84
< EELEC = -24274.7240 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24274.7240 EGB = 0.0000 RESTRAINT =
41.4034
> EAMBER (non-restraint) = -18216.8542
84c87
< Etot = -14371.2605 EKtot = 3843.8455 EPtot =
-18215.1060
---
> Etot = -14330.0477 EKtot = 3843.8455 EPtot =
-18173.8933
87c90,91
< EELEC = -24273.3960 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24273.3960 EGB = 0.0000 RESTRAINT =
41.2128
> EAMBER (non-restraint) = -18215.1060
90c94
< Etot = -14371.3474 EKtot = 3848.9511 EPtot =
-18220.2985
---
> Etot = -14330.2871 EKtot = 3848.9511 EPtot =
-18179.2382
93c97,98
< EELEC = -24272.3671 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24272.3671 EGB = 0.0000 RESTRAINT =
41.0603
> EAMBER (non-restraint) = -18220.2985
96c101
< Etot = -14371.4557 EKtot = 3859.3314 EPtot =
-18230.7872
---
> Etot = -14330.5031 EKtot = 3859.3314 EPtot =
-18189.8346
99c104,105
< EELEC = -24271.6192 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24271.6192 EGB = 0.0000 RESTRAINT =
40.9526
> EAMBER (non-restraint) = -18230.7872
102c108
< Etot = -14371.5396 EKtot = 3872.1405 EPtot =
-18243.6801
---
> Etot = -14330.6588 EKtot = 3872.1405 EPtot =
-18202.7993
105c111,112
< EELEC = -24270.6614 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24270.6614 EGB = 0.0000 RESTRAINT =
40.8808
> EAMBER (non-restraint) = -18243.6801
108c115
< Etot = -14371.4401 EKtot = 3884.4149 EPtot =
-18255.8550
---
> Etot = -14330.6005 EKtot = 3884.4149 EPtot =
-18215.0154
111c118,119
< EELEC = -24269.1041 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24269.1041 EGB = 0.0000 RESTRAINT =
40.8396
> EAMBER (non-restraint) = -18255.8550
114c122
< Etot = -14371.3442 EKtot = 3893.7656 EPtot =
-18265.1098
---
> Etot = -14330.5209 EKtot = 3893.7656 EPtot =
-18224.2865
117c125,126
< EELEC = -24267.0114 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24267.0114 EGB = 0.0000 RESTRAINT =
40.8233
> EAMBER (non-restraint) = -18265.1098
120c129
< Etot = -14371.0865 EKtot = 3898.7752 EPtot =
-18269.8617
---
> Etot = -14330.2612 EKtot = 3898.7752 EPtot =
-18229.0364
123c132,133
< EELEC = -24264.0719 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24264.0719 EGB = 0.0000 RESTRAINT =
40.8253
> EAMBER (non-restraint) = -18269.8617
127c137
< Etot = -14371.3416 EKtot = 3867.3184 EPtot =
-18238.6599
---
> Etot = -14330.1889 EKtot = 3867.3184 EPtot =
-18197.5073
130c140,141
< EELEC = -24272.1854 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = -24272.1854 EGB = 0.0000 RESTRAINT =
41.1527
> EAMBER (non-restraint) = -18238.6599
134c145
< Etot = 0.1555 EKtot = 18.9232 EPtot =
18.9344
---
> Etot = 0.3805 EKtot = 18.9232 EPtot =
19.1072
137c148,149
< EELEC = 4.7577 EGB = 0.0000 RESTRAINT =
0.0000
---
> EELEC = 4.7577 EGB = 0.0000 RESTRAINT =
0.3586
> EAMBER (non-restraint) = 18.7485
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Received on Mon Jun 27 2005 - 17:53:00 PDT