Re: Is there solution to numerical inaccuracy

From: Alok Juneja (juneja_at_speakeasy.net)
Date: Fri Nov 23 2007 - 12:14:01 CST

Dear Peter, Dave, Himanshu & other list member,

Sorry for not answering ealier though I was regularly following the
discussion on this issue. As requested by Peter, I am providing my

I am running constant temperature 50 ns dynamics, total of 25000000
steps with time step of 0.002ps and dcdfreq of 100 however restartfreq
of 100000. Some how my MD crashed at 5459300 but my last restrart was
5400000. I restarted with this. I am doing this MD to see the protein
behavious and am calculating the N and C terminal distance (Ang.).
Following is the N-C terminal distance before crash and after crash. I
am running this simulation in parallel.

# TIME(PS) Before-Crash After-Crash
10800 10.833
10800.2 11.3259 11.0924
10800.4 11.2417 11.1039
10800.6 10.985 10.9962
10800.8 10.7715 11.1593
10801 11.3783 11.4828
10801.2 11.1862 10.9861
10801.4 11.3925 10.9671
10801.6 10.8473 10.9287
(*) 10801.8 10.5789 11.013
10802 10.8792 10.4324
10802.2 10.6182 10.4422
10802.4 10.8918 10.6541
10802.6 10.9267 10.7829
10802.8 10.6352 10.8386
10803 10.8069 10.4295
(*) 10803.2 11.3242 10.5952
(*) 10803.4 11.3397 10.4784
(*) 10803.6 11.5822 10.4696
(*) 10803.8 11.023 10.8231
10804 10.9887 10.4586
10804.2 10.5118 10.3266
(*) 10804.4 10.4329 9.95989
10804.6 10.6863 10.2366
(*) 10804.8 11.3551 10.2149
(*) 10805 11.3445 9.88589
10805.2 10.7702 10.1757
10805.4 10.4436 10.3636
10805.6 10.3206 10.2086
10805.8 10.8214 10.5937
10806 11.2742 10.3849
10806.2 11.44 10.2721
(*) 10806.4 11.2566 10.1909
10806.6 10.9381 10.7606
10806.8 11.5617 10.8286
10807 11.7283 11.246
10807.2 11.4038 11.2901
10807.4 10.5862 10.708
10807.6 10.61 10.6308
10807.8 11.1818 10.2391
10808 11.3433 10.5278
10808.2 11.1947 11.0142
10808.4 10.9988 11.2578
(*) 10808.6 10.447 11.334
10808.8 10.3205 10.9368
10809 10.7634 10.9165
10809.2 10.7874 11.1041
10809.4 11.011 11.15
10809.6 10.8222 10.9214
10809.8 10.8731 10.2806
10810 11.0003 10.908

You will find so many time steps where the difference is remarkable
(indicated by *). I believe that this much of difference is too much for
me. I checked this is not the case with CHARMM where you get the
identical results even after restart.

Energy chart of the above showed time(ps): (Before Crash)

ENERGY: 5400000 28.7945 105.6469 71.1147
0.0000 -49041.3521 4585.4371 0.0000
0.0000 8054.3713 -36195.9876 296.8249
-36179.9317 -36177.7456 296.1387 -801.2118
-799.3909 140608.0000 -932.3294 -932.3120
ENERGY: 5400100 37.3399 105.0382 75.1800
0.0000 -48831.0494 4486.8740 0.0000
0.0000 8049.8831 -36076.7342 296.6595
-36059.3209 -36063.4089 295.1881 -1014.0289
-1018.0986 140608.0000 -822.2330 -822.1972
ENERGY: 5400200 24.1922 129.4631 75.4042
0.0000 -49035.3867 4700.6916 0.0000
0.0000 8089.0696 -36016.5660 298.1036
-35999.3292 -36001.8122 298.3934 -563.9091
-566.8751 140608.0000 -731.1942 -730.9017
ENERGY: 5400300 46.6230 108.8960 72.0267
0.0000 -48969.3991 4478.8393 0.0000
0.0000 8185.8140 -36077.2000 301.6689
-36060.9900 -36059.8814 298.5032 -1186.5489
-1181.0474 140608.0000 -830.1444 -830.2008
ENERGY: 5400400 35.9459 104.5525 75.6155
0.0000 -49109.6686 4711.4362 0.0000
0.0000 8068.2053 -36113.9132 297.3347
-36097.5827 -36095.5501 297.6449 -654.2566
-654.3221 140608.0000 -810.5780 -810.0556
ENERGY: 5400500 35.4348 107.8387 71.3716
0.0000 -49005.2470 4616.9064 0.0000
0.0000 8081.0662 -36092.6292 297.8087
-36075.9547 -36074.7717 298.0404 -916.9598
-920.2101 140608.0000 -598.2698 -597.5324
ENERGY: 5400600 33.4124 103.2531 74.2709
0.0000 -49211.8656 4778.3600 0.0000
0.0000 8171.6777 -36050.8915 301.1480
-36034.6998 -36031.4154 298.3279 -531.7955
-530.5480 140608.0000 -803.1952 -802.8407
ENERGY: 5400700 42.4858 103.1371 75.1335
0.0000 -49081.6646 4709.2067 0.0000
0.0000 8176.9712 -35974.7303 301.3430
-35958.0146 -35959.0132 299.2797 -591.6107
-596.0671 140608.0000 -651.6850 -652.0301
ENERGY: 5400800 43.7765 97.9494 72.5321
0.0000 -49087.9249 4769.0362 0.0000
0.0000 8189.5228 -35915.1079 301.8056
-35899.1317 -35896.3471 299.3696 -370.1239
-363.3212 140608.0000 -445.0617 -445.4932
ENERGY: 5400900 41.5001 112.2324 71.7137
0.0000 -49022.6856 4706.4816 0.0000
0.0000 8159.7951 -35930.9627 300.7100
-35914.2950 -35914.0196 299.5001 -496.1433
-493.5821 140608.0000 -561.2866 -560.6223
ENERGY: 5401000 47.8817 99.5306 71.0420
0.0000 -49067.7024 4664.9797 0.0000
0.0000 8148.9989 -36035.2695 300.3122
-36019.3311 -36015.9235 299.5215 -707.3898
-700.1092 140608.0000 -695.6862 -695.9468
ENERGY: 5401100 37.6674 102.9664 74.2476
0.0000 -49210.5135 4789.8270 0.0000
0.0000 8006.9694 -36198.8357 295.0780
-36181.8875 -36181.1417 297.0478 -503.3593
-505.7311 140608.0000 -449.2512 -449.2324
ENERGY: 5401200 43.0819 93.5302 75.9695
0.0000 -49215.2561 4686.6869 0.0000
0.0000 8129.9587 -36186.0290 299.6105
-36168.4346 -36170.7502 299.6291 -732.3619
-727.7515 140608.0000 -462.8188 -463.0718
ENERGY: 5401300 41.4914 103.4415 73.4675
0.0000 -49330.0252 4800.5243 0.0000
0.0000 8104.4127 -36206.6877 298.6691
-36191.0495 -36185.0947 299.7122 -515.6525
-516.1102 140608.0000 -475.5978 -475.7720
ENERGY: 5401400 38.1156 87.3639 74.0088
0.0000 -48985.3672 4558.2555 0.0000
0.0000 8075.1655 -36152.4580 297.5912
-36136.2210 -36134.4031 299.5468 -975.0929
-971.9640 140608.0000 -736.2508 -737.2321
ENERGY: 5401500 40.1361 95.7971 69.9930
0.0000 -49167.3997 4687.6305 0.0000
0.0000 8115.9464 -36157.8966 299.0941
-36141.5716 -36139.5561 297.6113 -696.2462
-689.6682 140608.0000 -800.5529 -800.1168
ENERGY: 5401600 36.2408 102.6551 69.0972
0.0000 -49300.7995 4809.8610 0.0000
0.0000 8126.4523 -36156.4931 299.4813
-36139.5243 -36139.9530 299.5567 -513.3946
-518.4773 140608.0000 -605.9198 -606.7441
ENERGY: 5401700 38.5107 104.4764 68.7909
0.0000 -49296.6517 4785.8258 0.0000
0.0000 8047.2070 -36251.8409 296.5609
-36234.2064 -36236.6000 297.1803 -578.2765
-571.4410 140608.0000 -596.5717 -597.0788
ENERGY: 5401800 27.9611 106.7028 68.4581
0.0000 -49206.8518 4706.0900 0.0000
0.0000 8095.1467 -36202.4930 298.3276
-36185.2219 -36188.2991 296.3223 -698.1896
-697.8902 140608.0000 -588.0123 -588.3609
ENERGY: 5401900 52.2575 98.0630 64.6628
0.0000 -49334.3105 4831.0558 0.0000
0.0000 7991.1595 -36297.1118 294.4954
-36279.4465 -36282.5447 297.3340 -484.1835
-478.5481 140608.0000 -637.1120 -637.3450
ENERGY: 5402000 36.2581 97.1192 69.9218
0.0000 -49276.6741 4666.1876 0.0000
0.0000 8113.3837 -36293.8037 298.9997
-36277.1145 -36277.5660 295.9792 -738.3546
-735.6172 140608.0000 -493.5679 -493.7895
ENERGY: 5402100 38.0749 96.4264 68.4615
0.0000 -49174.1011 4587.7704 0.0000
0.0000 8127.4359 -36255.9320 299.5175
-36238.5785 -36241.1515 296.8253 -969.7103
-971.4608 140608.0000 -899.4297 -899.9856
ENERGY: 5402200 38.7052 110.8596 71.9572
0.0000 -49009.1602 4607.3194 0.0000
0.0000 7988.1043 -36192.2146 294.3828
-36174.7073 -36177.6707 297.3825 -836.4581
-835.5397 140608.0000 -731.8763 -731.5588
ENERGY: 5402300 35.2297 113.8821 78.6378
0.0000 -49230.7859 4735.5967 0.0000
0.0000 8168.6473 -36098.7922 301.0363
-36081.7611 -36082.5655 299.2200 -604.3940
-606.6077 140608.0000 -711.0743 -710.4449
ENERGY: 5402400 43.4644 108.7022 75.4667
0.0000 -49086.9672 4649.8994 0.0000
0.0000 8207.1779 -36002.2566 302.4562
-35985.1139 -35987.1453 301.5592 -696.6126
-709.1234 140608.0000 -702.1451 -702.5027
ENERGY: 5402500 44.4436 117.1129 70.3500
0.0000 -49177.6722 4670.4326 0.0000
0.0000 8243.7464 -36031.5866 303.8039
-36013.2689 -36017.7422 302.3104 -797.6602
-801.9446 140608.0000 -797.5902 -797.2873
ENERGY: 5402600 42.6194 110.6687 67.3034
0.0000 -49096.0375 4738.3847 0.0000
0.0000 8148.3979 -35988.6633 300.2900
-35972.1823 -35972.4034 300.7834 -549.7226
-544.3715 140608.0000 -676.6325 -676.9192
ENERGY: 5402700 33.7540 109.5120 70.2248
0.0000 -49016.2711 4637.3564 0.0000
0.0000 8111.2281 -36054.1957 298.9202
-36037.1311 -36038.1426 299.6439 -761.6115
-755.2068 140608.0000 -484.5597 -484.0095
ENERGY: 5402800 31.9197 99.0958 66.3698
0.0000 -49055.6698 4733.5885 0.0000
0.0000 8053.3147 -36071.3813 296.7860
-36054.3287 -36055.2386 298.1713 -524.6244
-537.2706 140608.0000 -574.5815 -575.0480
ENERGY: 5402900 37.5170 116.0352 74.7081
0.0000 -49001.1194 4658.9854 0.0000
0.0000 8034.5462 -36079.3276 296.0943
-36063.0796 -36061.5579 298.1241 -696.3212
-701.7042 140608.0000 -621.5902 -621.2030
ENERGY: 5403000 29.7689 104.3031 71.5548
0.0000 -48941.4909 4539.8185 0.0000
0.0000 8173.6761 -36022.3696 301.2216
-36006.6379 -36004.3314 297.6805 -868.9589
-870.3128 140608.0000 -610.6720 -611.1378
ENERGY: 5403100 41.5888 114.6904 73.4357
0.0000 -49210.9001 4790.9052 0.0000
0.0000 8151.8985 -36038.3814 300.4190
-36023.9329 -36016.7353 300.6446 -547.6726
-542.2279 140608.0000 -622.4957 -622.7996
ENERGY: 5403200 48.9463 102.8697 70.1495
0.0000 -49075.6424 4612.4310 0.0000
0.0000 8151.8799 -36089.3659 300.4184
-36070.9041 -36078.2545 300.0950 -782.1712
-773.7714 140608.0000 -599.5890 -600.1843
ENERGY: 5403300 39.4471 100.1088 75.3412
0.0000 -48918.9453 4647.9520 0.0000
0.0000 8036.4063 -36019.6898 296.1628
-36001.7298 -36007.8646 298.2377 -641.5822
-637.5942 140608.0000 -704.2521 -704.6085
ENERGY: 5403400 47.5676 114.9005 69.3163
0.0000 -48870.1904 4530.9054 0.0000
0.0000 8082.2546 -36025.2460 297.8525
-36009.7572 -36005.3750 299.1902 -906.2337
-904.3834 140608.0000 -845.1238 -844.7908
ENERGY: 5403500 45.1770 110.1794 68.8276
0.0000 -49143.8195 4689.5885 0.0000
0.0000 8117.4885 -36112.5585 299.1509
-36096.1261 -36093.9231 299.7262 -675.7908
-673.6674 140608.0000 -669.8942 -669.3217
ENERGY: 5403600 32.4040 124.4383 70.5598
0.0000 -49274.9114 4829.6582 0.0000
0.0000 8113.7005 -36104.1505 299.0113
-36087.1428 -36088.0931 297.7506 -297.6637
-297.6209 140608.0000 -594.0219 -594.2362
ENERGY: 5403700 41.4582 102.2210 70.2554
0.0000 -48940.1021 4567.7871 0.0000
0.0000 8094.3358 -36064.0446 298.2977
-36047.3661 -36047.1410 298.0650 -897.1712
-888.2233 140608.0000 -725.5899 -725.3236
ENERGY: 5403800 35.1540 111.1225 69.5652
0.0000 -49037.1331 4597.2652 0.0000
0.0000 8103.4448 -36120.5815 298.6334
-36104.2606 -36102.8667 297.5311 -811.1871
-811.5670 140608.0000 -765.1483 -765.2420
ENERGY: 5403900 39.0349 102.9957 64.7567
0.0000 -48848.5428 4508.1843 0.0000
0.0000 7994.6779 -36138.8932 294.6250
-36124.0586 -36116.9113 296.2212 -864.5653
-867.6088 140608.0000 -860.8132 -860.1096
ENERGY: 5404000 38.7992 106.0935 78.8505
0.0000 -49055.2028 4578.5003 0.0000
0.0000 8008.9692 -36243.9901 295.1517
-36228.5758 -36223.6728 294.4093 -947.1495
-941.7588 140608.0000 -824.4529 -824.2306
ENERGY: 5404100 40.1409 101.2511 74.4564
0.0000 -49093.3453 4619.4708 0.0000
0.0000 8006.3491 -36251.6770 295.0552
-36233.5308 -36238.0879 294.2636 -874.2759
-874.1938 140608.0000 -915.4214 -915.7459
ENERGY: 5404200 28.9491 116.2965 68.0663
0.0000 -49057.5161 4601.5045 0.0000
0.0000 8065.8086 -36176.8911 297.2464
-36159.2356 -36164.5604 294.9928 -834.0223
-837.6794 140608.0000 -847.3834 -846.8939
ENERGY: 5404300 54.2476 99.0408 72.6638
0.0000 -48874.2843 4492.4577 0.0000
0.0000 8062.7293 -36093.1451 297.1329
-36076.8576 -36076.0012 297.0989 -917.8287
-923.4807 140608.0000 -671.8368 -671.9798
ENERGY: 5404400 34.4483 120.2816 73.2249
0.0000 -48925.2908 4591.8116 0.0000
0.0000 8102.3834 -36003.1410 298.5943
-35987.2875 -35985.2123 297.9725 -739.6441
-742.6431 140608.0000 -806.8861 -807.7123
ENERGY: 5404500 39.7311 122.3148 69.4442
0.0000 -49157.7573 4832.0141 0.0000
0.0000 8089.3752 -36004.8778 298.1149
-35989.4024 -35983.2674 299.9635 -349.6391
-345.5087 140608.0000 -678.3209 -677.7013
ENERGY: 5404600 38.8499 104.4257 70.2496
0.0000 -48998.6443 4587.2775 0.0000
0.0000 8159.1460 -36038.6956 300.6861
-36022.4203 -36019.7831 299.6701 -841.5353
-840.3592 140608.0000 -634.4922 -634.5433
ENERGY: 5404700 41.8403 108.2300 73.6046
0.0000 -48901.2210 4530.3495 0.0000
0.0000 8174.3853 -35972.8112 301.2477
-35956.4145 -35954.4588 299.5745 -927.6055
-922.4026 140608.0000 -829.5536 -829.5841
ENERGY: 5404800 44.2557 98.2379 69.2655
0.0000 -49101.9387 4739.5895 0.0000
0.0000 8067.2257 -36083.3643 297.2986
-36066.3893 -36066.0275 299.4984 -544.3089
-534.9822 140608.0000 -836.9393 -837.1878
ENERGY: 5404900 35.4952 106.9500 74.5435
0.0000 -49159.4352 4636.9431 0.0000
0.0000 8265.8089 -36039.6946 304.6169
-36021.8569 -36026.8113 300.7363 -703.9446
-703.8782 140608.0000 -573.8209 -574.6047
ENERGY: 5405000 46.0940 112.2346 70.2814
0.0000 -49097.9070 4711.8059 0.0000
0.0000 8036.5555 -36120.9357 296.1683
-36103.1177 -36108.8542 300.4005 -687.4552
-691.7239 140608.0000 -657.1810 -656.9773

Energy chart of the above showed time(ps): (After Crash)
ENERGY: 5400000 28.7945 105.6469 71.1147
0.0000 -49041.3521 4585.4371 0.0000
0.0000 8052.5851 -36197.7738 296.7591
-36181.0903 -36181.0903 296.7591 -800.2277
-799.5669 140608.0000 -800.2277 -799.5669
ENERGY: 5400100 35.0979 109.5703 74.0879
0.0000 -49000.8111 4664.0308 0.0000
0.0000 7930.0862 -36187.9379 292.2447
-36169.7211 -36175.4197 295.3610 -735.2792
-732.3522 140608.0000 -832.5121 -833.0035
ENERGY: 5400200 33.3380 116.3550 74.0084
0.0000 -49246.1783 4662.8434 0.0000
0.0000 8106.5420 -36253.0914 298.7475
-36236.1009 -36235.7918 297.5869 -726.1531
-722.8336 140608.0000 -789.4596 -789.3654
ENERGY: 5400300 46.2715 101.8731 67.7055
0.0000 -49275.3316 4719.2006 0.0000
0.0000 8015.2166 -36325.0642 295.3819
-36309.2735 -36305.7753 297.1892 -653.6451
-653.2003 140608.0000 -757.6189 -757.6626
ENERGY: 5400400 36.7301 96.3829 67.9828
0.0000 -49238.8147 4797.4797 0.0000
0.0000 7997.4748 -36242.7645 294.7281
-36227.9230 -36221.4241 295.9376 -504.2554
-512.2397 140608.0000 -679.2358 -679.2506
ENERGY: 5400500 36.5184 100.9421 72.7692
0.0000 -49258.7063 4717.1915 0.0000
0.0000 8140.5039 -36190.7810 299.9991
-36175.2262 -36171.0993 296.6951 -727.4620
-732.5021 140608.0000 -718.7720 -719.1169
ENERGY: 5400600 36.1507 94.2051 72.1415
0.0000 -49089.8105 4681.2568 0.0000
0.0000 8113.1081 -36092.9481 298.9895
-36075.3313 -36080.3889 297.6560 -611.7599
-612.5539 140608.0000 -707.0116 -707.3142
ENERGY: 5400700 38.3654 101.9681 76.7216
0.0000 -49163.0155 4770.8490 0.0000
0.0000 8053.9518 -36121.1596 296.8094
-36106.0839 -36099.6966 298.0376 -482.8220
-480.6048 140608.0000 -454.1956 -454.1254
ENERGY: 5400800 38.2993 103.3874 67.7375
0.0000 -49087.8620 4684.3457 0.0000
0.0000 8092.2190 -36101.8730 298.2197
-36084.9424 -36086.9313 298.8198 -629.2951
-638.0763 140608.0000 -646.1329 -646.4055
ENERGY: 5400900 27.2886 121.4140 70.0512
0.0000 -49103.8027 4719.2780 0.0000
0.0000 8062.6254 -36103.1455 297.1291
-36086.5396 -36086.2343 298.5030 -479.0495
-484.8091 140608.0000 -603.1613 -603.3016
ENERGY: 5401000 37.4879 116.5438 65.3268
0.0000 -48954.2813 4608.7188 0.0000
0.0000 8103.1592 -36023.0448 298.6229
-36007.6076 -36003.9412 298.9623 -738.0287
-742.8743 140608.0000 -767.4686 -766.3180
ENERGY: 5401100 35.0350 101.2840 63.7246
0.0000 -48784.4464 4493.4503 0.0000
0.0000 7989.3676 -36101.5850 294.4293
-36084.8559 -36084.9844 298.2325 -1019.8138
-1014.0656 140608.0000 -752.5389 -753.4042
ENERGY: 5401200 40.7283 104.2759 66.4073
0.0000 -49063.6823 4604.0619 0.0000
0.0000 8104.6139 -36143.5950 298.6765
-36127.7161 -36123.9145 296.6795 -837.3524
-839.4085 140608.0000 -787.0998 -786.7057
ENERGY: 5401300 31.9104 104.4965 73.4572
0.0000 -49039.4399 4642.6217 0.0000
0.0000 8099.7299 -36087.2241 298.4965
-36070.2025 -36072.1049 299.5192 -740.3261
-732.0814 140608.0000 -838.4230 -838.4131
ENERGY: 5401400 40.8109 96.2612 66.4647
0.0000 -49237.3078 4784.9583 0.0000
0.0000 8222.1148 -36026.6979 303.0067
-36012.0985 -36004.7920 299.7541 -498.3788
-499.8581 140608.0000 -541.4050 -541.2455
ENERGY: 5401500 33.1043 100.6185 66.9862
0.0000 -48932.9905 4643.5347 0.0000
0.0000 8117.6211 -35971.1257 299.1558
-35952.3377 -35959.5675 300.6900 -597.6145
-597.1506 140608.0000 -681.1095 -682.0617
ENERGY: 5401600 55.7657 104.7882 68.2414
0.0000 -49059.2057 4752.1728 0.0000
0.0000 8164.6957 -35913.5418 300.8906
-35897.7101 -35893.6048 301.5098 -488.1083
-484.7985 140608.0000 -627.5352 -627.5690
ENERGY: 5401700 37.4228 113.9139 68.5952
0.0000 -49204.1007 4848.5572 0.0000
0.0000 8221.9909 -35913.6207 303.0021
-35895.7867 -35899.1017 301.2891 -247.6396
-243.7463 140608.0000 -633.7711 -632.9802
ENERGY: 5401800 36.3077 113.3806 70.7545
0.0000 -49112.8260 4741.5292 0.0000
0.0000 8187.6441 -35963.2099 301.7364
-35945.5678 -35947.8362 300.9906 -538.3400
-554.0598 140608.0000 -594.5382 -594.7966
ENERGY: 5401900 50.2056 101.3733 69.7768
0.0000 -48794.3592 4556.3047 0.0000
0.0000 8048.7980 -35967.9008 296.6195
-35951.1493 -35950.7096 299.2159 -727.2276
-730.1196 140608.0000 -585.8002 -585.8311
ENERGY: 5402000 45.7264 105.5550 72.9403
0.0000 -48938.6290 4613.5916 0.0000
0.0000 8167.8145 -35933.0012 301.0056
-35917.0162 -35913.5752 299.6170 -668.6041
-666.5194 140608.0000 -571.5760 -572.4673
ENERGY: 5402100 33.5296 111.4058 71.4836
0.0000 -48960.2994 4671.1828 0.0000
0.0000 8164.5501 -35908.1475 300.8853
-35890.6231 -35892.8902 301.0813 -496.2655
-490.0098 140608.0000 -690.3000 -690.6535
ENERGY: 5402200 37.6993 120.3591 67.2097
0.0000 -48882.0363 4536.0921 0.0000
0.0000 8102.3371 -36018.3389 298.5926
-36002.3660 -35997.1126 301.4329 -846.9676
-850.8096 140608.0000 -638.7343 -638.5840
ENERGY: 5402300 32.1686 124.1655 66.4497
0.0000 -49264.4107 4768.3883 0.0000
0.0000 8226.9893 -36046.2493 303.1863
-36029.1598 -36029.3860 300.3612 -501.8299
-500.3960 140608.0000 -733.4133 -733.3089
ENERGY: 5402400 46.1753 105.1726 70.5889
0.0000 -49121.1778 4709.4560 0.0000
0.0000 8145.6893 -36044.0956 300.1902
-36028.6258 -36022.7734 300.5079 -671.8070
-681.3917 140608.0000 -453.8179 -453.8940
ENERGY: 5402500 37.0645 102.8940 73.7880
0.0000 -48946.3807 4566.1218 0.0000
0.0000 8147.9952 -36018.5172 300.2752
-36002.1537 -35999.1373 299.7113 -802.9509
-806.8127 140608.0000 -556.3944 -555.8124
ENERGY: 5402600 45.3871 112.3977 78.0488
0.0000 -48980.0262 4620.1117 0.0000
0.0000 8133.3189 -35990.7620 299.7343
-35972.6979 -35977.0235 299.5520 -809.2426
-808.0200 140608.0000 -723.6426 -723.7014
ENERGY: 5402700 43.4875 119.0184 73.3071
0.0000 -49032.5004 4668.9246 0.0000
0.0000 8154.6548 -35973.1080 300.5206
-35955.8490 -35957.7060 298.5774 -643.3800
-647.4327 140608.0000 -750.9940 -750.7380
ENERGY: 5402800 43.0868 114.1991 71.0842
0.0000 -49193.5263 4699.2125 0.0000
0.0000 8236.5884 -36029.3553 303.5401
-36011.7790 -36012.1099 302.2336 -694.5362
-691.2875 140608.0000 -625.3857 -624.5900
ENERGY: 5402900 44.2627 122.4830 76.9655
0.0000 -48979.7619 4578.1648 0.0000
0.0000 8080.6558 -36077.2303 297.7936
-36060.8501 -36059.4238 299.7771 -981.8171
-976.9715 140608.0000 -833.7604 -833.0853
ENERGY: 5403000 30.8737 112.3538 80.8453
0.0000 -49110.4089 4692.3011 0.0000
0.0000 8124.8915 -36069.1435 299.4238
-36052.0815 -36052.6961 296.9806 -597.8860
-603.0532 140608.0000 -926.0219 -926.9380
ENERGY: 5403100 48.0611 96.8124 76.9506
0.0000 -49177.0848 4687.6083 0.0000
0.0000 8135.4410 -36132.2114 299.8125
-36115.5838 -36114.9903 298.8324 -641.3925
-644.3619 140608.0000 -755.7657 -755.5849
ENERGY: 5403200 33.7850 107.7679 73.1474
0.0000 -49144.6602 4705.6138 0.0000
0.0000 8077.5128 -36146.8332 297.6777
-36129.7592 -36131.0901 297.7704 -707.8210
-713.8756 140608.0000 -638.0284 -637.3809
ENERGY: 5403300 37.3812 113.2705 79.2046
0.0000 -49020.2771 4551.8334 0.0000
0.0000 8178.8005 -36059.7869 301.4104
-36042.6468 -36045.4093 297.8679 -926.3334
-924.1989 140608.0000 -904.3347 -904.2558
ENERGY: 5403400 37.2458 117.2054 76.3314
0.0000 -49113.2321 4674.3063 0.0000
0.0000 8194.6459 -36013.4973 301.9944
-35997.0455 -35996.1896 299.4800 -671.7332
-676.6700 140608.0000 -800.9440 -800.7957
ENERGY: 5403500 37.4950 108.3049 80.7173
0.0000 -49174.0634 4761.2192 0.0000
0.0000 8124.9076 -36061.4194 299.4244
-36045.5121 -36040.6207 301.0619 -576.2367
-567.6970 140608.0000 -602.7510 -602.8105
ENERGY: 5403600 33.1284 110.2382 80.6756
0.0000 -49049.1675 4659.7979 0.0000
0.0000 8155.7739 -36009.5535 300.5619
-35991.1264 -35997.2975 300.3638 -660.8826
-664.7800 140608.0000 -536.3878 -536.6986
ENERGY: 5403700 45.1307 104.7599 76.7363
0.0000 -48959.6927 4600.6679 0.0000
0.0000 8193.0892 -35939.3087 301.9370
-35922.4494 -35923.1406 301.2004 -788.0595
-790.8388 140608.0000 -682.3214 -681.4332
ENERGY: 5403800 32.6815 118.1342 79.8366
0.0000 -49001.8444 4694.4070 0.0000
0.0000 8095.9739 -35980.8112 298.3581
-35964.9519 -35960.4259 299.2512 -532.6475
-536.5231 140608.0000 -667.8167 -668.2319
ENERGY: 5403900 40.3335 110.1377 75.7004
0.0000 -48930.2541 4687.1858 0.0000
0.0000 8052.3148 -35964.5819 296.7491
-35948.3938 -35945.6188 298.0477 -485.2634
-480.0421 140608.0000 -576.0339 -576.3751
ENERGY: 5404000 43.6209 102.3681 80.2898
0.0000 -48837.3784 4516.6082 0.0000
0.0000 8082.3521 -36012.1394 297.8561
-35993.9128 -35999.1412 297.4904 -845.1317
-853.0991 140608.0000 -759.3332 -758.7960
ENERGY: 5404100 32.3992 112.4978 76.2953
0.0000 -49282.6529 4819.6196 0.0000
0.0000 8167.9984 -36073.8425 301.0124
-36056.2897 -36058.6511 298.4186 -405.1396
-400.7609 140608.0000 -555.0593 -554.7751
ENERGY: 5404200 39.2157 110.9523 77.8316
0.0000 -49234.5852 4754.7409 0.0000
0.0000 8149.6513 -36102.1934 300.3362
-36084.9720 -36086.4221 300.0408 -631.7641
-620.3602 140608.0000 -611.3783 -611.0601
ENERGY: 5404300 40.2640 102.7402 76.5790
0.0000 -48946.6419 4632.5713 0.0000
0.0000 8028.3000 -36066.1874 295.8641
-36049.4042 -36049.1796 299.2763 -722.4619
-722.7303 140608.0000 -604.9384 -604.9460
ENERGY: 5404400 38.4378 103.8227 78.6116
0.0000 -49181.5875 4742.1218 0.0000
0.0000 8165.5886 -36053.0050 300.9236
-36035.2820 -36039.4711 298.7135 -503.3298
-510.9613 140608.0000 -676.3273 -676.7852
ENERGY: 5404500 32.4573 108.8940 70.9985
0.0000 -49140.4844 4661.6868 0.0000
0.0000 8158.5977 -36107.8502 300.6659
-36089.5725 -36095.3760 298.5895 -747.4275
-749.9198 140608.0000 -702.4612 -702.4456
ENERGY: 5404600 32.5747 112.8289 70.2502
0.0000 -49264.9270 4773.3487 0.0000
0.0000 8124.6122 -36151.3124 299.4135
-36134.7078 -36135.1241 298.0471 -532.7230
-536.1898 140608.0000 -702.7731 -703.5772
ENERGY: 5404700 34.2222 108.8330 72.2308
0.0000 -49177.9121 4669.3590 0.0000
0.0000 8237.8687 -36055.3983 303.5873
-36038.1833 -36041.0689 299.6331 -678.2061
-686.1844 140608.0000 -598.2731 -598.4207
ENERGY: 5404800 41.0464 106.3744 72.8643
0.0000 -49197.8170 4743.4738 0.0000
0.0000 8201.3472 -36032.7110 302.2414
-36016.4297 -36013.2738 300.2671 -551.9281
-551.4829 140608.0000 -498.4708 -498.7667
ENERGY: 5404900 43.7664 88.2393 77.9591
0.0000 -48998.6807 4618.7050 0.0000
0.0000 7998.8938 -36171.1170 294.7804
-36153.8117 -36156.0421 295.8946 -753.5119
-753.2144 140608.0000 -808.5867 -808.4087
ENERGY: 5405000 33.5948 100.7013 70.3891
0.0000 -49061.4438 4624.8433 0.0000
0.0000 8094.8533 -36137.0620 298.3168
-36120.3271 -36120.0671 297.8987 -753.3383
-746.4889 140608.0000 -727.4415 -726.8773

For your ready reference, I am attaching the total energy graph for easy
comparision (comparision.pdf).
As requested by Dave, I am attaching file A-B1-B2.pdf, the job run on
single same processor.

Test A
ENERGY: 0 44.7528 98.8199 77.6169
0.0000 -49345.3261 5695.1920 0.0000
0.0000 8177.6755 -35251.2689 301.2366
-35234.0780 -35234.0780 301.2366 1539.1129
1540.3649 140608.0000 1539.1129 1540.3649
ENERGY: 100 34.3119 96.9733 76.8311
0.0000 -48058.3080 4200.5671 0.0000
0.0000 8260.4489 -35389.1756 304.2857
-35372.5197 -35372.6991 302.8211 -1229.6681
-1226.6885 140608.0000 -454.5524 -454.9376
ENERGY: 200 40.2822 100.8266 74.6310
0.0000 -48404.8028 4580.4608 0.0000
0.0000 8155.8038 -35452.7985 300.4309
-35436.3946 -35434.8320 303.1510 -625.9539
-626.6145 140608.0000 -797.5277 -797.1145
ENERGY: 300 39.0889 104.1516 74.5543
0.0000 -48464.8054 4564.4193 0.0000
0.0000 8151.7738 -35530.8176 300.2825
-35514.1587 -35514.1614 300.7083 -614.4220
-626.1203 140608.0000 -712.3121 -712.4860
ENERGY: 400 40.4266 106.6642 74.0429
0.0000 -48430.4090 4566.2519 0.0000
0.0000 8084.3153 -35558.7081 297.7976
-35541.2885 -35544.1973 298.8030 -723.7596
-718.2771 140608.0000 -803.9054 -803.7946
ENERGY: 500 40.0808 95.8208 76.3873
0.0000 -48869.2480 4816.5273 0.0000
0.0000 8200.6381 -35639.7937 302.0825
-35621.7612 -35624.5212 301.8578 -234.8964
-238.3923 140608.0000 -506.1887 -507.1056
ENERGY: 600 44.0046 97.5326 76.3955
0.0000 -48525.9730 4516.4419 0.0000
0.0000 8114.4519 -35677.1463 298.9077
-35661.2572 -35656.8166 301.2198 -885.6710
-886.9142 140608.0000 -553.4151 -552.6843
ENERGY: 700 39.5246 97.2873 76.5272
0.0000 -48665.6756 4658.5870 0.0000
0.0000 8024.1227 -35769.6268 295.5803
-35753.7626 -35751.2992 298.3329 -626.7679
-629.6501 140608.0000 -752.4783 -753.1436
ENERGY: 800 40.6087 105.1842 76.4158
0.0000 -48637.7304 4574.9204 0.0000
0.0000 8056.8473 -35783.7541 296.7857
-35768.9984 -35763.0584 298.4907 -722.8790
-718.0264 140608.0000 -691.8396 -691.8337
ENERGY: 900 36.2956 97.4623 78.2799
0.0000 -48638.1075 4620.7330 0.0000
0.0000 8062.5092 -35742.8274 296.9943
-35727.2188 -35724.8105 297.5696 -761.9235
-762.0080 140608.0000 -852.6779 -852.5704
ENERGY: 1000 43.3060 103.6871 81.2541
0.0000 -48595.4223 4507.0856 0.0000
0.0000 8059.9429 -35800.1465 296.8998
-35785.6189 -35778.5303 297.6671 -837.5445
-831.0595 140608.0000 -712.0840 -712.1978

TestB1
ENERGY: 0 44.7528 98.8199 77.6169
0.0000 -49345.3261 5695.1920 0.0000
0.0000 8177.6755 -35251.2689 301.2366
-35234.0780 -35234.0780 301.2366 1539.1129
1540.3649 140608.0000 1539.1129 1540.3649
ENERGY: 100 34.3119 96.9733 76.8311
0.0000 -48058.3080 4200.5671 0.0000
0.0000 8260.4489 -35389.1756 304.2857
-35372.5197 -35372.6991 302.8211 -1229.6681
-1226.6885 140608.0000 -454.5524 -454.9376
ENERGY: 200 40.2822 100.8266 74.6310
0.0000 -48404.8028 4580.4608 0.0000
0.0000 8155.8038 -35452.7985 300.4309
-35436.3946 -35434.8320 303.1510 -625.9539
-626.6145 140608.0000 -797.5277 -797.1145
ENERGY: 300 39.0889 104.1516 74.5543
0.0000 -48464.8054 4564.4193 0.0000
0.0000 8151.7738 -35530.8176 300.2825
-35514.1587 -35514.1614 300.7083 -614.4220
-626.1203 140608.0000 -712.3121 -712.4860
ENERGY: 400 40.4266 106.6642 74.0429
0.0000 -48430.4090 4566.2519 0.0000
0.0000 8084.3153 -35558.7081 297.7976
-35541.2885 -35544.1973 298.8030 -723.7596
-718.2771 140608.0000 -803.9054 -803.7946
ENERGY: 500 40.0808 95.8208 76.3873
0.0000 -48869.2480 4816.5273 0.0000
0.0000 8200.6381 -35639.7937 302.0825
-35621.7612 -35624.5212 301.8578 -234.8964
-238.3923 140608.0000 -506.1887 -507.1056

TestB2
ENERGY: 500 40.0808 95.8208 76.3873
0.0000 -48869.2480 4816.5273 0.0000
0.0000 8198.1801 -35642.2517 301.9919
-35624.8476 -35624.8476 301.9919 -240.5321
-239.4591 140608.0000 -240.5321 -239.4591
ENERGY: 600 44.1071 99.4043 73.9469
0.0000 -48645.9056 4504.8343 0.0000
0.0000 8201.1240 -35722.4891 302.1004
-35704.5165 -35708.1228 300.9174 -945.7516
-947.1788 140608.0000 -548.3354 -547.9895
ENERGY: 700 36.9480 116.2777 74.2721
0.0000 -48424.1899 4498.2627 0.0000
0.0000 8064.8668 -35633.5625 297.0811
-35615.9610 -35618.7113 299.6434 -880.2162
-879.5000 140608.0000 -791.9282 -792.8730
ENERGY: 800 40.0158 93.7852 77.3175
0.0000 -48767.4622 4764.0734 0.0000
0.0000 8110.8778 -35681.3926 298.7760
-35663.2181 -35668.8405 298.9492 -425.9056
-423.3385 140608.0000 -629.7279 -629.2701
ENERGY: 900 31.7891 103.3564 73.0194
0.0000 -48585.5909 4523.4754 0.0000
0.0000 8125.4342 -35728.5165 299.3122
-35711.5863 -35712.9202 298.7923 -879.4512
-875.0408 140608.0000 -599.0120 -598.8936
ENERGY: 1000 39.1487 102.3842 75.2077
0.0000 -48668.2244 4629.8116 0.0000
0.0000 8082.9538 -35738.7184 297.7474
-35721.5901 -35724.0567 298.8931 -651.8244
-647.8176 140608.0000 -892.2844 -891.4353

Best Wishes,
Alok

Peter Freddolino wrote:

>Just as an addendum, namd's random number generation is no longer
>deterministic in parallel; this means that Langevin dynamics will be
>deterministic and as repeatable as an NVE simulation *if* you use the
>same seed an run in serial, but not otherwise (see the comment in the
>namd manual on the seed parameter). In either case you're limited by
>floating point addition, as Dave described.
>Peter
>
>David Hardy wrote:
>
>
>>You can control the sequence of random numbers generated by choosing
>>the seed (although I don't know the method that NAMD employs to
>>generate random numbers in parallel). This part of the algorithm is
>>deterministic.
>>
>>My earlier comment actually applies to NVE simulation with no "random"
>>component. Since Hamiltonian systems are chaotic, any small
>>perturbation (from the non-associativity of addition) can cause
>>deviation from a previous trajectory.
>>
>>-Dave
>>
>>
>>On Nov 22, 2007, at 2:19 AM, Himanshu Khandelia wrote:
>>
>>
>>
>>>>Hi,
>>>>
>>>>
>>>>For different parallel runs, NAMD will perform
>>>>non-deterministically, in the
>>>>sense that the order of completion of different processors (and even
>>>>the work
>>>>that is assigned to them) will likely change, altering the order of
>>>>summed
>>>>energies. Due to the non-associativity of floating point addition,
>>>>you should
>>>>eventually see slightly different energy values from two parallel
>>>>runs of an
>>>>identical trajectory.
>>>>
>>>>
>>>I thought the non-reproducibility of simulations in NAMD was mainly
>>>because of the Berendsen pressure controller employed, which gives
>>>random
>>>kicks to particles every few steps. Whether or not the run is
>>>parallel, I
>>>do not think the trajectories will be reproducible, although I have not
>>>tested this myself.
>>>
>>>
>>>
>>----------------------------------------------------------
>>David J. Hardy, PhD
>>Theoretical and Computational Biophysics
>>Beckman Institute, University of Illinois
>>dhardy_at_ks.uiuc.edu
>>http://www.ks.uiuc.edu/~dhardy/
>>
>>
>
>
>
>
>

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