AMBER Archive (2006)

Subject: Re: AMBER: Test Failure during amber9 serial compilation

From: Ray Luo (rluo_at_uci.edu)
Date: Tue Apr 25 2006 - 13:01:49 CDT

We'll take a look of this with gcc 4.02, on Pentium FC3 to see whether
we can reproduce your problem.

Thomas Steinbrecher wrote:

> Dear amber users,
>
> I have compiled and tested a version of amber9 using gcc 4.0.2 on an
> Athlon Suse Linux system. While most of the tests in the test suite
> PASSED, apart from rounding problems one FAILURE seemed to be severe:
>
> The Run.pbpgb test in pb_pgb/ fails with temperatures rising to
> unreasonably high values in the test run (Please see attached .dif file).
>
> Can someone suggest to me what might be the cause for this problem?
>
> Something similar (also in the pb_pgb test) is described for amber8 at
> http://structbio.vanderbilt.edu/archives/amber-archive/2005/2300.php
> and bugfix.45 modified the pb_pgb test. However in my case running the
> test produces very unrealistic results, so I believe there is some
> other problem.
>
> I'd be happy about any suggestion,
>
> Kind Regards,
>
> Thomas
>
>------------------------------------------------------------------------
>
>67,68c67,68
>< NSTEP = 1 TIME(PS) = 4.011 TEMP(K) = 301.06 PRESS = 0.
>< Etot = -14327.0777 EKtot = 3899.5186 EPtot = -18226.5964
>---
>
>
>> NSTEP = 1 TIME(PS) = 4.011 TEMP(K) = 303.59 PRESS = 0.
>> Etot = -14294.2980 EKtot = 3932.2984 EPtot = -18226.5964
>>
>>
>75,143c75,143
>< NSTEP = 2 TIME(PS) = 4.012 TEMP(K) = 300.90 PRESS = 0.
>< Etot = -14327.9991 EKtot = 3897.3806 EPtot = -18225.3797
>< BOND = 90.0779 ANGLE = 264.9066 DIHED = 313.4493
>< 1-4 NB = 196.9372 1-4 EEL = 3040.2513 VDWAALS = 2083.4632
>< EELEC = -24255.3196 EPB = 0. RESTRAINT = 40.8544
>< ECAVITY= 0. EDISPER = 0.
>< EAMBER (non-restraint) = -18266.2341
>< ------------------------------------------------------------------------------
>< NSTEP = 3 TIME(PS) = 4.013 TEMP(K) = 300.64 PRESS = 0.
>< Etot = -14328.5631 EKtot = 3894.0614 EPtot = -18222.6245
>< BOND = 92.5127 ANGLE = 267.7280 DIHED = 312.5051
>< 1-4 NB = 196.7205 1-4 EEL = 3037.9438 VDWAALS = 2081.7358
>< EELEC = -24252.6437 EPB = 0. RESTRAINT = 40.8732
>< ECAVITY= 0. EDISPER = 0.
>< EAMBER (non-restraint) = -18263.4977
>< ------------------------------------------------------------------------------
>< NSTEP = 4 TIME(PS) = 4.014 TEMP(K) = 300.43 PRESS = 0.
>< Etot = -14328.2051 EKtot = 3891.2656 EPtot = -18219.4707
>< BOND = 94.9651 ANGLE = 269.8086 DIHED = 311.9042
>< 1-4 NB = 196.5035 1-4 EEL = 3035.6880 VDWAALS = 2080.0704
>< EELEC = -24249.2987 EPB = 0. RESTRAINT = 40.8884
>< ECAVITY= 0. EDISPER = 0.
>< EAMBER (non-restraint) = -18260.3591
>< ------------------------------------------------------------------------------
>< NSTEP = 5 TIME(PS) = 4.015 TEMP(K) = 300.35 PRESS = 0.
>< Etot = -14328.2980 EKtot = 3890.3015 EPtot = -18218.5995
>< BOND = 97.1107 ANGLE = 270.3701 DIHED = 311.6839
>< 1-4 NB = 196.2664 1-4 EEL = 3033.4874 VDWAALS = 2078.5345
>< EELEC = -24246.9529 EPB = 0. RESTRAINT = 40.9003
>< ECAVITY= 0. EDISPER = 0.
>< EAMBER (non-restraint) = -18259.4999
>< ------------------------------------------------------------------------------
>< NSTEP = 6 TIME(PS) = 4.016 TEMP(K) = 300.46 PRESS = 0.
>< Etot = -14327.8950 EKtot = 3891.6989 EPtot = -18219.5939
>< BOND = 98.8960 ANGLE = 269.1553 DIHED = 311.8379
>< 1-4 NB = 196.0030 1-4 EEL = 3031.3366 VDWAALS = 2077.1932
>< EELEC = -24244.9223 EPB = 0. RESTRAINT = 40.9064
>< ECAVITY= 0. EDISPER = 0.
>< EAMBER (non-restraint) = -18260.5003
>< ------------------------------------------------------------------------------
>< NSTEP = 7 TIME(PS) = 4.017 TEMP(K) = 300.74 PRESS = 0.
>< Etot = -14328.4873 EKtot = 3895.2981 EPtot = -18223.7854
>< BOND = 100.4730 ANGLE = 266.4844 DIHED = 312.3253
>< 1-4 NB = 195.7214 1-4 EEL = 3029.2240 VDWAALS = 2076.1978
>< EELEC = -24245.1152 EPB = 0. RESTRAINT = 40.9039
>< ECAVITY= 0. EDISPER = 0.
>< EAMBER (non-restraint) = -18264.6894
>< ------------------------------------------------------------------------------
>< NSTEP = 8 TIME(PS) = 4.018 TEMP(K) = 301.11 PRESS = 0.
>< Etot = -14328.0583 EKtot = 3900.0981 EPtot = -18228.1564
>< BOND = 102.0580 ANGLE = 263.1416 DIHED = 313.0839
>< 1-4 NB = 195.4407 1-4 EEL = 3027.1353 VDWAALS = 2075.6007
>< EELEC = -24245.5053 EPB = 0. RESTRAINT = 40.8888
>< ECAVITY= 0. EDISPER = 0.
>< EAMBER (non-restraint) = -18269.0452
>< ------------------------------------------------------------------------------
>< NSTEP = 9 TIME(PS) = 4.019 TEMP(K) = 301.47 PRESS = 0.
>< Etot = -14328.0992 EKtot = 3904.8378 EPtot = -18232.9370
>< BOND = 103.7796 ANGLE = 260.1353 DIHED = 314.0416
>< 1-4 NB = 195.1853 1-4 EEL = 3025.0582 VDWAALS = 2075.4377
>< EELEC = -24247.4297 EPB = 0. RESTRAINT = 40.8550
>< ECAVITY= 0. EDISPER = 0.
>< EAMBER (non-restraint) = -18273.7920
>< ------------------------------------------------------------------------------
>< NSTEP = 10 TIME(PS) = 4.020 TEMP(K) = 301.78 PRESS = 0.
>< Etot = -14328.3803 EKtot = 3908.8218 EPtot = -18237.2021
>< BOND = 105.5821 ANGLE = 258.4054 DIHED = 315.1270
>< 1-4 NB = 194.9792 1-4 EEL = 3022.9853 VDWAALS = 2075.7062
>< EELEC = -24250.7898 EPB = 0. RESTRAINT = 40.8024
>---
>
>
>> NSTEP = 2 TIME(PS) = 4.012 TEMP(K) = 324.27 PRESS = 0.
>> Etot = -13992.4586 EKtot = 4200.1436 EPtot = -18192.6021
>> BOND = 89.1882 ANGLE = 268.2156 DIHED = 313.6217
>> 1-4 NB = 196.7650 1-4 EEL = 3040.2071 VDWAALS = 2079.8791
>> EELEC = -24221.2807 EPB = 0. RESTRAINT = 40.8019
>> ECAVITY= 0. EDISPER = 0.
>> EAMBER (non-restraint) = -18233.4040
>> ------------------------------------------------------------------------------
>> NSTEP = 3 TIME(PS) = 4.013 TEMP(K) = 366.53 PRESS = 0.
>> Etot = -13365.5176 EKtot = 4747.4932 EPtot = -18113.0108
>> BOND = 92.7701 ANGLE = 277.9097 DIHED = 313.0418
>> 1-4 NB = 196.2246 1-4 EEL = 3037.8496 VDWAALS = 2071.0271
>> EELEC = -24142.5421 EPB = 0. RESTRAINT = 40.7084
>> ECAVITY= 0. EDISPER = 0.
>> EAMBER (non-restraint) = -18153.7192
>> ------------------------------------------------------------------------------
>> NSTEP = 4 TIME(PS) = 4.014 TEMP(K) = 429.69 PRESS = 0.
>> Etot = -12406.2724 EKtot = 5565.5018 EPtot = -17971.7742
>> BOND = 103.6711 ANGLE = 291.1204 DIHED = 313.0596
>> 1-4 NB = 195.5722 1-4 EEL = 3035.5907 VDWAALS = 2058.7598
>> EELEC = -24010.0964 EPB = 0. RESTRAINT = 40.5484
>> ECAVITY= 0. EDISPER = 0.
>> EAMBER (non-restraint) = -18012.3226
>> ------------------------------------------------------------------------------
>> NSTEP = 5 TIME(PS) = 4.015 TEMP(K) = 512.04 PRESS = 0.
>> Etot = -11112.7543 EKtot = 6632.2638 EPtot = -17745.0180
>> BOND = 127.0118 ANGLE = 307.6647 DIHED = 313.8248
>> 1-4 NB = 194.8365 1-4 EEL = 3033.4948 VDWAALS = 2043.2189
>> EELEC = -23805.3867 EPB = 0. RESTRAINT = 40.3171
>> ECAVITY= 0. EDISPER = 0.
>> EAMBER (non-restraint) = -17785.3352
>> ------------------------------------------------------------------------------
>> NSTEP = 6 TIME(PS) = 4.016 TEMP(K) = 610.44 PRESS = 0.
>> Etot = -9498.5178 EKtot = 7906.7178 EPtot = -17405.2356
>> BOND = 165.9801 ANGLE = 327.2098 DIHED = 315.4915
>> 1-4 NB = 194.0587 1-4 EEL = 3031.6146 VDWAALS = 2024.5467
>> EELEC = -23504.1571 EPB = 0. RESTRAINT = 40.0202
>> ECAVITY= 0. EDISPER = 0.
>> EAMBER (non-restraint) = -17445.2558
>> ------------------------------------------------------------------------------
>> NSTEP = 7 TIME(PS) = 4.017 TEMP(K) = 720.05 PRESS = 0.
>> Etot = -7606.4250 EKtot = 9326.4225 EPtot = -16932.8475
>> BOND = 219.9874 ANGLE = 348.9335 DIHED = 318.1809
>> 1-4 NB = 193.2839 1-4 EEL = 3029.9737 VDWAALS = 2003.0248
>> EELEC = -23085.9059 EPB = 0. RESTRAINT = 39.6743
>> ECAVITY= 0. EDISPER = 0.
>> EAMBER (non-restraint) = -16972.5218
>> ------------------------------------------------------------------------------
>> NSTEP = 8 TIME(PS) = 4.018 TEMP(K) = 834.63 PRESS = 0.
>> Etot = -5504.2451 EKtot = 10810.6000 EPtot = -16314.8450
>> BOND = 283.9942 ANGLE = 371.3402 DIHED = 321.9529
>> 1-4 NB = 192.5537 1-4 EEL = 3028.5913 VDWAALS = 1978.8176
>> EELEC = -22531.4164 EPB = 0. RESTRAINT = 39.3214
>> ECAVITY= 0. EDISPER = 0.
>> EAMBER (non-restraint) = -16354.1664
>> ------------------------------------------------------------------------------
>> NSTEP = 9 TIME(PS) = 4.019 TEMP(K) = 947.06 PRESS = 0.
>> Etot = -3286.7240 EKtot = 12266.8180 EPtot = -15553.5420
>> BOND = 349.3210 ANGLE = 392.3965 DIHED = 326.7457
>> 1-4 NB = 191.9006 1-4 EEL = 3027.4766 VDWAALS = 1952.1010
>> EELEC = -21832.5880 EPB = 0. RESTRAINT = 39.1047
>> ECAVITY= 0. EDISPER = 0.
>> EAMBER (non-restraint) = -15592.6467
>> ------------------------------------------------------------------------------
>> NSTEP = 10 TIME(PS) = 4.020 TEMP(K) = 1050.31 PRESS = 0.
>> Etot = -1061.2752 EKtot = 13604.2129 EPtot = -14665.4881
>> BOND = 405.7538 ANGLE = 409.9340 DIHED = 332.3593
>> 1-4 NB = 191.3437 1-4 EEL = 3026.6321 VDWAALS = 1923.0148
>> EELEC = -20993.7057 EPB = 0. RESTRAINT = 39.1798
>>
>>
>145c145
>< EAMBER (non-restraint) = -18278.0045
>---
>
>
>> EAMBER (non-restraint) = -14704.6679
>>
>>
>148,152c148,152
>< NSTEP = 10 TIME(PS) = 4.020 TEMP(K) = 300.89 PRESS = 0.
>< Etot = -14328.1063 EKtot = 3897.3282 EPtot = -18225.4346
>< BOND = 97.3654 ANGLE = 265.2568 DIHED = 313.0611
>< 1-4 NB = 196.0938 1-4 EEL = 3032.5706 VDWAALS = 2078.9155
>< EELEC = -24249.5688 EPB = 0. RESTRAINT = 40.8711
>---
>
>
>> NSTEP = 10 TIME(PS) = 4.020 TEMP(K) = 609.86 PRESS = 0.
>> Etot = -9212.8488 EKtot = 7899.2472 EPtot = -17112.0960
>> BOND = 192.5876 ANGLE = 325.7157 DIHED = 318.2931
>> 1-4 NB = 194.3720 1-4 EEL = 3033.4027 VDWAALS = 2021.9606
>> EELEC = -23238.4790 EPB = 0. RESTRAINT = 40.0514
>>
>>
>154c154
>< EAMBER (non-restraint) = -18266.3056
>---
>
>
>> EAMBER (non-restraint) = -17152.1474
>>
>>
>157,161c157,161
>< NSTEP = 10 TIME(PS) = 4.020 TEMP(K) = 0.45 PRESS = 0.
>< Etot = 0.3990 EKtot = 5.7756 EPtot = 5.7492
>< BOND = 5.5605 ANGLE = 3.9424 DIHED = 1.1617
>< 1-4 NB = 0.7159 1-4 EEL = 6.2411 VDWAALS = 3.3696
>< EELEC = 4.2396 EPB = 0. RESTRAINT = 0.0319
>---
>
>
>> NSTEP = 10 TIME(PS) = 4.020 TEMP(K) = 254.36 PRESS = 0.
>> Etot = 4446.3592 EKtot = 3294.5468 EPtot = 1171.3122
>> BOND = 111.1654 ANGLE = 50.2803 DIHED = 6.3290
>> 1-4 NB = 1.9640 1-4 EEL = 5.2388 VDWAALS = 53.3541
>> EELEC = 1065.2783 EPB = 0. RESTRAINT = 0.6529
>>
>>
>163c163
>< EAMBER (non-restraint) = 5.7174
>---
>
>
>> EAMBER (non-restraint) = 1170.6593
>>
>> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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